1 | [GENERAL] |
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2 | description = Rattus norvegicus |
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3 | database = scaffolds |
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4 | |
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5 | initial landmark = chr19:143000..180000 |
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6 | |
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7 | default tracks = Genes |
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8 | |
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9 | # examples to show in the introduction |
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10 | examples = chr1 |
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11 | chr1:80,000..120,000 |
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12 | |
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13 | # "automatic" classes to try when an unqualified identifier is given |
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14 | automatic classes = Symbol Gene Clone ID |
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15 | |
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16 | |
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17 | # try to configure the rubberband menu to query for eQTLs |
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18 | |
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19 | [DETAIL SELECT MENU] |
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20 | width = 250 |
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21 | html = <table style="width:100%"> |
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22 | <tr> |
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23 | <th style="background:lightgrey;cell-padding:5"> |
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24 | SELECTION |
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25 | <span style="right:0px;position:absolute;color:blue;cursor:pointer" |
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26 | onclick="SelectArea.prototype.cancelRubber()"> |
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27 | [X] |
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28 | </span> |
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29 | </th> |
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30 | </tr> |
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31 | <tr> |
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32 | <td> |
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33 | <span style="color:blue;cursor:pointer" onclick="SelectArea.prototype.clearAndSubmit()"> |
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34 | Zoom in |
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35 | </span> |
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36 | </td> |
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37 | </tr> |
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38 | <tr> |
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39 | <td> |
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40 | <span style="color:blue;cursor:pointer" onclick="SelectArea.prototype.clearAndRecenter()"> |
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41 | Recenter on this region |
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42 | </span> |
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43 | </td> |
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44 | </tr> |
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45 | <tr> |
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46 | <td onmouseup="SelectArea.prototype.cancelRubber()"> |
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47 | <a href="?plugin=FastaDumper;plugin_action=Go;name=SELECTION" target="_BLANK"> |
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48 | Dump selection as FASTA |
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49 | </a> |
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50 | </td> |
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51 | </tr> |
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52 | <tr> |
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53 | <td onmouseup="SelectArea.prototype.cancelRubber()"> |
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54 | <a href="/cgi-bin/eqtls/eqtls.py?action=list&what=markers&p=0.05&name=SELECTION" target="_BLANK"> |
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55 | eQTL markers in selection |
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56 | </a> |
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57 | </td> |
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58 | </tr> |
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59 | <tr> |
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60 | <td onmouseup="SelectArea.prototype.cancelRubber()"> |
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61 | <a href="/cgi-bin/eqtls/eqtls.py?action=list&what=transcripts&p=0.05&name=SELECTION" target="_BLANK"> |
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62 | eQTL transcripts in selection |
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63 | </a> |
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64 | </td> |
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65 | </tr> |
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66 | <tr> |
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67 | <td onmouseup="SelectArea.prototype.cancelRubber()"> |
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68 | <a href="/cgi-bin/eqtls.py?find=cis" target="_BLANK"> |
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69 | cis eQTLs in selection |
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70 | </a> |
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71 | </td> |
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72 | </tr> |
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73 | <tr> |
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74 | <td onmouseup="SelectArea.prototype.cancelRubber()"> |
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75 | <a href="/cgi-bin/coding-snps/codingsnps.pl?name=SELECTION" target="_BLANK"> |
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76 | coding SNPs in selection |
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77 | </a> |
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78 | </td> |
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79 | </tr> |
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80 | <tr> |
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81 | <td onmouseup="SelectArea.prototype.cancelRubber()"> |
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82 | <a href="http://vm7.target.rug.nl/xqtl_unstable/api/find/org.molgenis.xgap.Marker?name=SELECTION" target="_BLANK"> |
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83 | molgenis region query |
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84 | </a> |
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85 | </td> |
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86 | </tr> |
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87 | </table> |
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88 | |
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89 | ### |
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90 | ### The last entry in the menu list is a molgenis example which creates urls: |
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91 | ### .../api/find/org.molgenis.xgap.Marker?name=chr1:3790000..4759999 |
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92 | |
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93 | ################################# |
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94 | # database definitions |
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95 | ################################# |
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96 | |
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97 | [scaffolds:database] |
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98 | db_adaptor = Bio::DB::SeqFeature::Store |
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99 | db_args = -adaptor DBI::mysql |
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100 | -dsn dbi:mysql:database=rn4 |
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101 | -user apache |
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102 | |
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103 | [variations:database] |
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104 | db_adaptor = Bio::DB::SeqFeature::Store |
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105 | db_args = -adaptor DBI::mysql |
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106 | -dsn dbi:mysql:database=rn4_variations |
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107 | -user apache |
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108 | |
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109 | # for the SNP density plots |
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110 | aggregators = snp_density{bin:SNP:SHR} |
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111 | |
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112 | |
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113 | ############################################################################### |
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114 | ### Rbm 20 databasese |
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115 | |
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116 | |
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117 | [rbm20_cluster:database] |
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118 | db_adaptor = Bio::DB::SeqFeature::Store |
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119 | db_args = -adaptor DBI::mysql |
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120 | -dsn dbi:mysql:database=rn4_rbm20_cluster |
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121 | -user apache |
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122 | |
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123 | |
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124 | # [rbm20:database] |
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125 | # db_adaptor = Bio::DB::SeqFeature::Store |
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126 | # db_args = -adaptor DBI::mysql |
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127 | # -dsn dbi:mysql:database=rn4_rbm20 |
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128 | # -user apache |
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129 | |
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130 | #[rbm20-mutant:database] |
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131 | #db_adaptor = Bio::DB::Sam |
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132 | #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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133 | # -bam /var/www/html/gbrowse2/databases/rn4/rbm20/rawreadsmutant-bowtie-sorted.bam.bam |
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134 | #search options = default |
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135 | # |
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136 | [rbm20-wildtype:database] |
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137 | db_adaptor = Bio::DB::Sam |
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138 | db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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139 | -bam /var/www/html/gbrowse2/databases/rn4/rbm20/wildtype.bam |
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140 | search options = default |
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141 | |
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142 | #[rbm20-mutant-fwd:database] |
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143 | #db_adaptor = Bio::DB::Sam |
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144 | #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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145 | # -bam /var/www/html/gbrowse2/databases/rn4/rbm20/rawreadsmutant-bowtie-sorted.bam.bam |
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146 | #search options = default |
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147 | # |
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148 | #[rbm20-wildtype-fwd:database] |
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149 | #db_adaptor = Bio::DB::Sam |
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150 | #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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151 | # -bam /var/www/html/gbrowse2/databases/rn4/rbm20/rawreadswildtype-bowtie-sorted.bam.bam |
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152 | #search options = default |
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153 | # |
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154 | #[rbm20-mutant-rev:database] |
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155 | #db_adaptor = Bio::DB::Sam |
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156 | #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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157 | # -bam /var/www/html/gbrowse2/databases/rn4/rbm20/rawreadsmutant-bowtie-sorted.bam.bam |
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158 | #search options = default |
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159 | # |
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160 | #[rbm20-wildtype-rev:database] |
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161 | #db_adaptor = Bio::DB::Sam |
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162 | #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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163 | # -bam /var/www/html/gbrowse2/databases/rn4/rbm20/rawreadswildtype-bowtie-sorted.bam.bam |
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164 | #search options = default |
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165 | |
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166 | |
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167 | |
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168 | ############################################################################### |
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169 | ### histone modification databases |
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170 | |
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171 | [histones:database] |
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172 | db_adaptor = Bio::DB::SeqFeature::Store |
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173 | db_args = -adaptor DBI::mysql |
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174 | -dsn dbi:mysql:database=rn4_histones |
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175 | -user apache |
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176 | |
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177 | [histones_h3k27me3:database] |
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178 | db_adaptor = Bio::DB::SeqFeature::Store |
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179 | db_args = -adaptor DBI::mysql |
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180 | -dsn dbi:mysql:database=rn4_histones_h3k27me3 |
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181 | -user apache |
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182 | |
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183 | |
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184 | # |
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185 | [lv-H3K4me3-BN-male-bio2-tech1:database] |
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186 | db_adaptor = Bio::DB::Sam |
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187 | db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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188 | -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K4me3-BN-male-bio2-tech1-rmdup.bam |
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189 | |
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190 | [lv-H3K4me3-SHR-male-bio2-tech1:database] |
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191 | db_adaptor = Bio::DB::Sam |
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192 | db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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193 | -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K4me3-SHR-male-bio2-tech1-rmdup.bam |
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194 | |
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195 | [lv-H3K4me3-BN-female-bio1-tech1:database] |
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196 | db_adaptor = Bio::DB::Sam |
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197 | db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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198 | -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K4me3-BN-female-bio1-tech1-rmdup.bam |
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199 | |
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200 | [lv-H3K4me3-SHR-female-bio1-tech1:database] |
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201 | db_adaptor = Bio::DB::Sam |
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202 | db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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203 | -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K4me3-SHR-female-bio1-tech1-rmdup.bam |
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204 | |
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205 | [lv-H3K27me3-BN-male-bio2-merged:database] |
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206 | db_adaptor = Bio::DB::Sam |
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207 | db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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208 | -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K27me3-BN-male-bio2-merged.bam |
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209 | |
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210 | [lv-H3K27me3-BN-male-bio3-merged:database] |
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211 | db_adaptor = Bio::DB::Sam |
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212 | db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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213 | -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K27me3-BN-male-bio3-merged.bam |
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214 | |
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215 | [lv-H3K27me3-BN-male-bio4-merged:database] |
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216 | db_adaptor = Bio::DB::Sam |
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217 | db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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218 | -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K27me3-BN-male-bio4-merged.bam |
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219 | |
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220 | |
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221 | |
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222 | [BN-H3K4me3:database] |
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223 | db_adaptor = Bio::DB::Sam |
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224 | db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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225 | -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/BN-H3K4me3-sorted.bam |
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226 | search options = default |
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227 | |
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228 | [BN-H3K27me3:database] |
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229 | db_adaptor = Bio::DB::Sam |
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230 | db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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231 | -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/BN-H3K27me3-sorted.bam |
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232 | search options = default |
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233 | |
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234 | [BN-input:database] |
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235 | db_adaptor = Bio::DB::Sam |
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236 | db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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237 | -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/BN-input-sorted.bam |
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238 | search options = default |
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239 | |
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240 | [SHR-H3K4me3:database] |
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241 | db_adaptor = Bio::DB::Sam |
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242 | db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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243 | -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/SHR-H3K4me3-sorted.bam |
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244 | search options = default |
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245 | |
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246 | [SHR-H3K27me3:database] |
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247 | db_adaptor = Bio::DB::Sam |
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248 | db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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249 | -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/SHR-H3K27me3-sorted.bam |
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250 | search options = default |
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251 | |
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252 | [SHR-input:database] |
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253 | db_adaptor = Bio::DB::Sam |
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254 | db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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255 | -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/SHR-input-sorted.bam |
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256 | search options = default |
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257 | |
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258 | |
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259 | [BXH12-H3K4:database] |
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260 | db_adaptor = Bio::DB::Sam |
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261 | db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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262 | -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/K4-BXH12_sorted.bam |
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263 | search options = default |
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264 | |
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265 | [BXH02-H3K4:database] |
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266 | db_adaptor = Bio::DB::Sam |
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267 | db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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268 | -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/K4-BXH02_sorted.bam |
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269 | search options = default |
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270 | |
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271 | [BXH03-H3K4:database] |
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272 | db_adaptor = Bio::DB::Sam |
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273 | db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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274 | -bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/K4-BXH03.bam |
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275 | search options = default |
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276 | |
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277 | ############################################################################### |
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278 | ### micro rna databases |
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279 | |
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280 | [BN-mirna:database] |
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281 | db_adaptor = Bio::DB::Sam |
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282 | db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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283 | -bam /var/www/html/gbrowse2/databases/rn4/mirna/BN.csfasta__sorted.bam |
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284 | search options = default |
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285 | |
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286 | #[HXB01-mirna:database] |
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287 | #db_adaptor = Bio::DB::Sam |
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288 | #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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289 | #-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB01.csfasta__sorted.bam |
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290 | #search options = default |
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291 | |
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292 | #[HXB03-mirna:database] |
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293 | #db_adaptor = Bio::DB::Sam |
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294 | #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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295 | #-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB03.csfasta__sorted.bam |
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296 | #search options = default |
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297 | |
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298 | #[HXB05-mirna:database] |
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299 | #db_adaptor = Bio::DB::Sam |
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300 | #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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301 | #-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB05.csfasta__sorted.bam |
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302 | #search options = default |
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303 | |
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304 | #[HXB10-mirna:database] |
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305 | #db_adaptor = Bio::DB::Sam |
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306 | #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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307 | #-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB10.csfasta__sorted.bam |
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308 | #search options = default |
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309 | |
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310 | #[HXB15-mirna:database] |
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311 | #db_adaptor = Bio::DB::Sam |
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312 | #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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313 | #-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB15.csfasta__sorted.bam |
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314 | #search options = default |
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315 | |
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316 | #[HXB18-mirna:database] |
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317 | #db_adaptor = Bio::DB::Sam |
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318 | #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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319 | #-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB18.csfasta__sorted.bam |
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320 | #search options = default |
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321 | |
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322 | #[HXB21-mirna:database] |
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323 | #db_adaptor = Bio::DB::Sam |
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324 | #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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325 | #-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB21.csfasta__sorted.bam |
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326 | #search options = default |
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327 | |
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328 | #[HXB23-mirna:database] |
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329 | #db_adaptor = Bio::DB::Sam |
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330 | #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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331 | #-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB23.csfasta__sorted.bam |
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332 | #search options = default |
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333 | |
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334 | #[HXB25-mirna:database] |
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335 | #db_adaptor = Bio::DB::Sam |
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336 | #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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337 | #-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB25.csfasta__sorted.bam |
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338 | #search options = default |
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339 | |
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340 | #[HXB29-mirna:database] |
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341 | #db_adaptor = Bio::DB::Sam |
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342 | #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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343 | #-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB29.csfasta__sorted.bam |
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344 | #search options = default |
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345 | |
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346 | #[SHR-mirna:database] |
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347 | #db_adaptor = Bio::DB::Sam |
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348 | #db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa |
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349 | #-bam /var/www/html/gbrowse2/databases/rn4/mirna/SHR.csfasta__sorted.bam |
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350 | #search options = default |
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351 | |
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352 | |
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353 | |
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354 | ############################################################################### |
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355 | ### track configurations |
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356 | |
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357 | # Default glyph settings |
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358 | [TRACK DEFAULTS] |
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359 | glyph = generic |
---|
360 | database = scaffolds |
---|
361 | height = 8 |
---|
362 | bgcolor = cyan |
---|
363 | fgcolor = black |
---|
364 | label density = 25 |
---|
365 | bump density = 100 |
---|
366 | |
---|
367 | ### TRACK CONFIGURATION #### |
---|
368 | # the remainder of the sections configure individual tracks |
---|
369 | |
---|
370 | |
---|
371 | # view the reads |
---|
372 | |
---|
373 | ############################################################################### |
---|
374 | ### histone modifications track configurations |
---|
375 | |
---|
376 | |
---|
377 | # for the sex specific analysis |
---|
378 | [Coverage-lv-H3K4me3-BN-female-bio1-tech1] |
---|
379 | feature = coverage |
---|
380 | glyph = wiggle_xyplot |
---|
381 | database = lv-H3K4me3-BN-female-bio1-tech1 |
---|
382 | height = 50 |
---|
383 | fgcolor = black |
---|
384 | bgcolor = indigo |
---|
385 | key = Coverage lv-H3K4me3-BN-female-bio1-tech1 |
---|
386 | category = Histone modifications |
---|
387 | label = 0 # Labels on wiggle tracks are redundant. |
---|
388 | |
---|
389 | [Coverage-lv-H3K4me3-SHR-female-bio1-tech1] |
---|
390 | feature = coverage |
---|
391 | glyph = wiggle_xyplot |
---|
392 | database = lv-H3K4me3-SHR-female-bio1-tech1 |
---|
393 | height = 50 |
---|
394 | fgcolor = black |
---|
395 | bgcolor = indigo |
---|
396 | key = Coverage lv-H3K4me3-SHR-female-bio1-tech1 |
---|
397 | category = Histone modifications |
---|
398 | label = 0 # Labels on wiggle tracks are redundant. |
---|
399 | |
---|
400 | [lv-H3K4me3-BN-male-bio2-tech1] |
---|
401 | feature = coverage |
---|
402 | glyph = wiggle_xyplot |
---|
403 | database = lv-H3K4me3-BN-male-bio2-tech1 |
---|
404 | height = 50 |
---|
405 | fgcolor = black |
---|
406 | bgcolor = indigo |
---|
407 | key = Coverage lv-H3K4me3-BN-male-bio2-tech1 |
---|
408 | category = Histone modifications |
---|
409 | label = 0 # Labels on wiggle tracks are redundant. |
---|
410 | |
---|
411 | [lv-H3K4me3-SHR-male-bio2-tech1-rmdup] |
---|
412 | feature = coverage |
---|
413 | glyph = wiggle_xyplot |
---|
414 | database = lv-H3K4me3-SHR-male-bio2-tech1 |
---|
415 | height = 50 |
---|
416 | fgcolor = black |
---|
417 | bgcolor = indigo |
---|
418 | key = Coverage lv-H3K4me3-SHR-male-bio2-tech1 |
---|
419 | category = Histone modifications |
---|
420 | label = 0 # Labels on wiggle tracks are redundant. |
---|
421 | |
---|
422 | |
---|
423 | |
---|
424 | |
---|
425 | |
---|
426 | # BN |
---|
427 | [Coverage-lv-H3K27me3-BN-male-bio2-merged] |
---|
428 | feature = coverage |
---|
429 | glyph = wiggle_xyplot |
---|
430 | database = lv-H3K27me3-BN-male-bio2-merged |
---|
431 | height = 50 |
---|
432 | fgcolor = black |
---|
433 | bgcolor = indigo |
---|
434 | key = Coverage lv-H3K27me3-BN-male-bio2-merged |
---|
435 | category = Histone modifications |
---|
436 | label = 0 # Labels on wiggle tracks are redundant. |
---|
437 | |
---|
438 | [Coverage-lv-H3K27me3-BN-male-bio3-merged] |
---|
439 | feature = coverage |
---|
440 | glyph = wiggle_xyplot |
---|
441 | database = lv-H3K27me3-BN-male-bio3-merged |
---|
442 | height = 50 |
---|
443 | fgcolor = black |
---|
444 | bgcolor = indigo |
---|
445 | key = Coverage lv-H3K27me3-BN-male-bio3-merged |
---|
446 | category = Histone modifications |
---|
447 | label = 0 # Labels on wiggle tracks are redundant. |
---|
448 | |
---|
449 | [Coverage-lv-H3K27me3-BN-male-bio4-merged] |
---|
450 | feature = coverage |
---|
451 | glyph = wiggle_xyplot |
---|
452 | database = lv-H3K27me3-BN-male-bio4-merged |
---|
453 | height = 50 |
---|
454 | fgcolor = black |
---|
455 | bgcolor = indigo |
---|
456 | key = Coverage lv-H3K27me3-BN-male-bio4-merged |
---|
457 | category = Histone modifications |
---|
458 | label = 0 # Labels on wiggle tracks are redundant. |
---|
459 | |
---|
460 | |
---|
461 | [Coverage-BN-H3K4me3] |
---|
462 | feature = coverage |
---|
463 | glyph = wiggle_xyplot |
---|
464 | database = BN-H3K4me3 |
---|
465 | height = 50 |
---|
466 | fgcolor = black |
---|
467 | bgcolor = indigo |
---|
468 | key = Coverage BN-H3K4me3 |
---|
469 | category = Histone modifications |
---|
470 | label = 0 # Labels on wiggle tracks are redundant. |
---|
471 | |
---|
472 | # [Coverage-BN-H3K27me3] |
---|
473 | # feature = coverage |
---|
474 | # glyph = wiggle_xyplot |
---|
475 | # database = BN-H3K27me3 |
---|
476 | # height = 50 |
---|
477 | # fgcolor = black |
---|
478 | # bgcolor = indigo |
---|
479 | # key = Coverage BN-H3K27me3 |
---|
480 | # category = Histone modifications |
---|
481 | # label = 0 # Labels on wiggle tracks are redundant. |
---|
482 | |
---|
483 | [Coverage-BN-input] |
---|
484 | feature = coverage |
---|
485 | glyph = wiggle_xyplot |
---|
486 | database = BN-input |
---|
487 | height = 50 |
---|
488 | fgcolor = black |
---|
489 | bgcolor = indigo |
---|
490 | key = Coverage BN-input |
---|
491 | category = Histone modifications |
---|
492 | label = 0 # Labels on wiggle tracks are redundant. |
---|
493 | |
---|
494 | # [Reads-BN-H3K4me3] |
---|
495 | # feature = match |
---|
496 | # glyph = segments |
---|
497 | # draw_target = 1 |
---|
498 | # show_mismatch = 1 |
---|
499 | # mismatch_color = red |
---|
500 | # database = BN-H3K4me3 |
---|
501 | # bgcolor = blue |
---|
502 | # fgcolor = blue |
---|
503 | # height = 5 |
---|
504 | # label density = 50 |
---|
505 | # bump = fast |
---|
506 | # key = Reads BN-H3K4me3 |
---|
507 | # category = Histone modifications |
---|
508 | # |
---|
509 | # [Reads-BN-H3K27me3] |
---|
510 | # feature = match |
---|
511 | # glyph = segments |
---|
512 | # draw_target = 1 |
---|
513 | # show_mismatch = 1 |
---|
514 | # mismatch_color = red |
---|
515 | # database = BN-H3K27me3 |
---|
516 | # bgcolor = blue |
---|
517 | # fgcolor = blue |
---|
518 | # height = 5 |
---|
519 | # label density = 50 |
---|
520 | # bump = fast |
---|
521 | # key = Reads BN-H3K27me3 |
---|
522 | # category = Histone modifications |
---|
523 | # |
---|
524 | # [Reads-BN-input] |
---|
525 | # feature = match |
---|
526 | # glyph = segments |
---|
527 | # draw_target = 1 |
---|
528 | # show_mismatch = 1 |
---|
529 | # mismatch_color = red |
---|
530 | # database = BN-input |
---|
531 | # bgcolor = blue |
---|
532 | # fgcolor = blue |
---|
533 | # height = 5 |
---|
534 | # label density = 50 |
---|
535 | # bump = fast |
---|
536 | # key = Reads BN-input |
---|
537 | # category = Histone modifications |
---|
538 | |
---|
539 | |
---|
540 | # SHR reads |
---|
541 | |
---|
542 | [Coverage-SHR-H3K4me3] |
---|
543 | feature = coverage |
---|
544 | glyph = wiggle_xyplot |
---|
545 | database = SHR-H3K4me3 |
---|
546 | height = 50 |
---|
547 | fgcolor = black |
---|
548 | bgcolor = indigo |
---|
549 | key = Coverage SHR-H3K4me3 |
---|
550 | category = Histone modifications |
---|
551 | label = 0 # Labels on wiggle tracks are redundant. |
---|
552 | |
---|
553 | |
---|
554 | [Coverage-SHR-input] |
---|
555 | feature = coverage |
---|
556 | glyph = wiggle_xyplot |
---|
557 | database = SHR-input |
---|
558 | height = 50 |
---|
559 | fgcolor = black |
---|
560 | bgcolor = indigo |
---|
561 | key = Coverage SHR-input |
---|
562 | category = Histone modifications |
---|
563 | label = 0 # Labels on wiggle tracks are redundant. |
---|
564 | |
---|
565 | # [Reads-SHR-H3K4me3] |
---|
566 | # feature = match |
---|
567 | # glyph = segments |
---|
568 | # draw_target = 1 |
---|
569 | # show_mismatch = 1 |
---|
570 | # mismatch_color = red |
---|
571 | # database = SHR-H3K4me3 |
---|
572 | # bgcolor = blue |
---|
573 | # fgcolor = blue |
---|
574 | # height = 5 |
---|
575 | # label density = 50 |
---|
576 | # bump = fast |
---|
577 | # key = Reads SHR-H3K4me3 |
---|
578 | # category = Histone modifications |
---|
579 | # |
---|
580 | # [Reads-SHR-H3K27me3] |
---|
581 | # feature = match |
---|
582 | # glyph = segments |
---|
583 | # draw_target = 1 |
---|
584 | # show_mismatch = 1 |
---|
585 | # mismatch_color = red |
---|
586 | # database = SHR-H3K27me3 |
---|
587 | # bgcolor = blue |
---|
588 | # fgcolor = blue |
---|
589 | # height = 5 |
---|
590 | # label density = 50 |
---|
591 | # bump = fast |
---|
592 | # key = Reads SHR-H3K27me3 |
---|
593 | # category = Histone modifications |
---|
594 | # |
---|
595 | # [Reads-SHR-input] |
---|
596 | # feature = match |
---|
597 | # glyph = segments |
---|
598 | # draw_target = 1 |
---|
599 | # show_mismatch = 1 |
---|
600 | # mismatch_color = red |
---|
601 | # database = SHR-input |
---|
602 | # bgcolor = blue |
---|
603 | # fgcolor = blue |
---|
604 | # height = 5 |
---|
605 | # label density = 50 |
---|
606 | # bump = fast |
---|
607 | # key = Reads SHR-input |
---|
608 | # category = Histone modifications |
---|
609 | # |
---|
610 | # |
---|
611 | # # reads for the RI strains |
---|
612 | # [Coverage-BXH12-H3K4me3] |
---|
613 | # feature = coverage |
---|
614 | # glyph = wiggle_xyplot |
---|
615 | # database = BXH12-H3K4 |
---|
616 | # height = 50 |
---|
617 | # fgcolor = black |
---|
618 | # bgcolor = indigo |
---|
619 | # key = Coverage BXH12-H3K4 |
---|
620 | # category = Histone modifications |
---|
621 | # label = 0 # Labels on wiggle tracks are redundant. |
---|
622 | # |
---|
623 | # [Reads-BXH12-H3K4me3] |
---|
624 | # feature = match |
---|
625 | # glyph = segments |
---|
626 | # draw_target = 1 |
---|
627 | # show_mismatch = 1 |
---|
628 | # mismatch_color = red |
---|
629 | # database = BXH12-H3K4 |
---|
630 | # bgcolor = blue |
---|
631 | # fgcolor = blue |
---|
632 | # height = 5 |
---|
633 | # label density = 50 |
---|
634 | # bump = fast |
---|
635 | # key = Reads BXH12-H3K4me3 |
---|
636 | # category = Histone modifications |
---|
637 | # |
---|
638 | # |
---|
639 | # [Coverage-BXH02-H3K4me3] |
---|
640 | # feature = coverage |
---|
641 | # glyph = wiggle_xyplot |
---|
642 | # database = BXH02-H3K4 |
---|
643 | # height = 50 |
---|
644 | # fgcolor = black |
---|
645 | # bgcolor = indigo |
---|
646 | # key = Coverage BXH102-H3K4 |
---|
647 | # category = Histone modifications |
---|
648 | # label = 0 # Labels on wiggle tracks are redundant. |
---|
649 | # |
---|
650 | # [Reads-BXH02-H3K4me3] |
---|
651 | # feature = match |
---|
652 | # glyph = segments |
---|
653 | # draw_target = 1 |
---|
654 | # show_mismatch = 1 |
---|
655 | # mismatch_color = red |
---|
656 | # database = BXH02-H3K4 |
---|
657 | # bgcolor = blue |
---|
658 | # fgcolor = blue |
---|
659 | # height = 5 |
---|
660 | # label density = 50 |
---|
661 | # bump = fast |
---|
662 | # key = Reads BXH02-H3K4me3 |
---|
663 | # category = Histone modifications |
---|
664 | # |
---|
665 | # [Coverage-BXH03-H3K4me3] |
---|
666 | # feature = coverage |
---|
667 | # glyph = wiggle_xyplot |
---|
668 | # database = BXH03-H3K4 |
---|
669 | # height = 50 |
---|
670 | # fgcolor = black |
---|
671 | # bgcolor = indigo |
---|
672 | # key = Coverage BXH103-H3K4 |
---|
673 | # category = Histone modifications |
---|
674 | # label = 0 # Labels on wiggle tracks are redundant. |
---|
675 | # |
---|
676 | # |
---|
677 | # [Reads-BXH03-H3K4me3] |
---|
678 | # feature = match |
---|
679 | # glyph = segments |
---|
680 | # draw_target = 1 |
---|
681 | # show_mismatch = 1 |
---|
682 | # mismatch_color = red |
---|
683 | # database = BXH03-H3K4 |
---|
684 | # bgcolor = blue |
---|
685 | # fgcolor = blue |
---|
686 | # height = 5 |
---|
687 | # label density = 50 |
---|
688 | # bump = fast |
---|
689 | # key = Reads BXH03-H3K4me3 |
---|
690 | # category = Histone modifications |
---|
691 | # |
---|
692 | # |
---|
693 | # # view the results of the island calling and differential analysis |
---|
694 | # [sicer-BN-H3K4me3] |
---|
695 | # feature = experimental_feature:sicer-BN-H3K4me3 |
---|
696 | # database = histones |
---|
697 | # glyph = generic |
---|
698 | # bgcolor = red |
---|
699 | # forwardcolor = red |
---|
700 | # reversecolor = red |
---|
701 | # key = Sicer BN-H3K4me3 |
---|
702 | # category = Histone modifications |
---|
703 | # |
---|
704 | # [sicer-BN-H3K27me3] |
---|
705 | # feature = experimental_feature:sicer-BN-H3K27me3 |
---|
706 | # database = histones |
---|
707 | # glyph = generic |
---|
708 | # bgcolor = red |
---|
709 | # forwardcolor = red |
---|
710 | # reversecolor = red |
---|
711 | # key = Sicer BN-H3K27me3 |
---|
712 | # category = Histone modifications |
---|
713 | # |
---|
714 | # [sicer-BN-input] |
---|
715 | # feature = experimental_feature:sicer-BN-input |
---|
716 | # database = histones |
---|
717 | # glyph = generic |
---|
718 | # bgcolor = red |
---|
719 | # forwardcolor = red |
---|
720 | # reversecolor = red |
---|
721 | # key = Sicer BN-input |
---|
722 | # category = Histone modifications |
---|
723 | # |
---|
724 | # [sicer-SHR-H3K4me3] |
---|
725 | # feature = experimental_feature:sicer-SHR-H3K4me3 |
---|
726 | # database = histones |
---|
727 | # glyph = generic |
---|
728 | # bgcolor = red |
---|
729 | # forwardcolor = red |
---|
730 | # reversecolor = red |
---|
731 | # key = Sicer SHR-H3K4me3 |
---|
732 | # category = Histone modifications |
---|
733 | # |
---|
734 | # [sicer-SHR-H3K27me3] |
---|
735 | # feature = experimental_feature:sicer-SHR-H3K27me3 |
---|
736 | # database = histones |
---|
737 | # glyph = generic |
---|
738 | # bgcolor = red |
---|
739 | # forwardcolor = red |
---|
740 | # reversecolor = red |
---|
741 | # key = Sicer SHR-H3K27me3 |
---|
742 | # category = Histone modifications |
---|
743 | # |
---|
744 | # [sicer-SHR-input] |
---|
745 | # feature = experimental_feature:sicer-SHR-input |
---|
746 | # database = histones |
---|
747 | # glyph = generic |
---|
748 | # bgcolor = red |
---|
749 | # forwardcolor = red |
---|
750 | # reversecolor = red |
---|
751 | # key = Sicer SHR-input |
---|
752 | # category = Histone modifications |
---|
753 | # |
---|
754 | # [chipdiff-H3K4me3] |
---|
755 | # feature = experimental_feature:chipdiff-H3K4me3 |
---|
756 | # database = histones |
---|
757 | # glyph = generic |
---|
758 | # bgcolor = red |
---|
759 | # forwardcolor = red |
---|
760 | # reversecolor = red |
---|
761 | # key = Chipdiff H3K4me3 |
---|
762 | # category = Histone modifications |
---|
763 | # |
---|
764 | # [chipdiff-H3K27me3] |
---|
765 | # feature = experimental_feature:chipdiff-H3K27me3 |
---|
766 | # database = histones |
---|
767 | # glyph = generic |
---|
768 | # bgcolor = red |
---|
769 | # forwardcolor = red |
---|
770 | # reversecolor = red |
---|
771 | # key = Chipdiff H3K27me3 |
---|
772 | # category = Histone modifications |
---|
773 | # |
---|
774 | # |
---|
775 | # # tracks for the peak calls in the RI strains |
---|
776 | # [sicer-H3K4-BXH02] |
---|
777 | # feature = experimental_feature:sicer-K4-BXH02 |
---|
778 | # database = histones |
---|
779 | # glyph = generic |
---|
780 | # bgcolor = red |
---|
781 | # forwardcolor = red |
---|
782 | # reversecolor = red |
---|
783 | # key = Sicer H3K4 BXH02 |
---|
784 | # category = Histone modifications |
---|
785 | # |
---|
786 | # |
---|
787 | # [sicer-H3K4-BXH12] |
---|
788 | # feature = experimental_feature:sicer-K4-BXH12 |
---|
789 | # database = histones |
---|
790 | # glyph = generic |
---|
791 | # bgcolor = red |
---|
792 | # forwardcolor = red |
---|
793 | # reversecolor = red |
---|
794 | # key = Sicer H3K4 BXH12 |
---|
795 | # category = Histone modifications |
---|
796 | # |
---|
797 | |
---|
798 | |
---|
799 | ############################################################################### |
---|
800 | ### Binned H3K27me3 data |
---|
801 | |
---|
802 | # [binned-lv-H3K27me3-BN-male-bio4-merged-offset-3750] |
---|
803 | # feature = microarray_oligo:lv-H3K27me3-BN-male-bio4-merged-offset-3750 |
---|
804 | # database = histones_h3k27me3 |
---|
805 | # glyph = wiggle_xyplot |
---|
806 | # smoothing = none |
---|
807 | # autoscale = local |
---|
808 | # bgcolor = indigo |
---|
809 | # height = 50 |
---|
810 | # graph_type = boxes |
---|
811 | # scale = right |
---|
812 | # description = 1 |
---|
813 | # category = Binned H3k27me3 data |
---|
814 | # key = lv-H3K27me3-BN-male-bio4-merged-offset-3750 |
---|
815 | # |
---|
816 | # [posterior-lv-H3K27me3-BN-male-bio4-merged-offset-3750] |
---|
817 | # feature = microarray_oligo:lv-H3K27me3-BN-male-bio4-merged-offset-3750-hmm |
---|
818 | # database = histones_h3k27me3 |
---|
819 | # glyph = wiggle_xyplot |
---|
820 | # smoothing = none |
---|
821 | # autoscale = global |
---|
822 | # bicolor_pivot = 0.99 |
---|
823 | # pos_color = red |
---|
824 | # neg_color = gray |
---|
825 | # height = 25 |
---|
826 | # graph_type = boxes |
---|
827 | # scale = right |
---|
828 | # description = 1 |
---|
829 | # category = Binned H3k27me3 data |
---|
830 | # key = lv-H3K27me3-BN-male-bio4-merged-offset-3750-hmm |
---|
831 | |
---|
832 | #[binned-binsize-5000-posterior-lv-H3K27me3-BN-male-bio2-merged-avg-posterior] |
---|
833 | #feature = microarray_oligo:lv-H3K27me3-BN-male-bio2-merged-avg-posterior-binsize-5000 |
---|
834 | #database = histones_h3k27me3 |
---|
835 | #glyph = wiggle_xyplot |
---|
836 | #smoothing = none |
---|
837 | #autoscale = global |
---|
838 | #bicolor_pivot = 0.99 |
---|
839 | #pos_color = red |
---|
840 | #neg_color = gray |
---|
841 | #height = 25 |
---|
842 | #graph_type = boxes |
---|
843 | #scale = right |
---|
844 | #description = 1 |
---|
845 | #category = Binned H3k27me3 data |
---|
846 | #key = lv-H3K27me3-BN-male-bio2-merged-hmm-avg-binsize-5000 |
---|
847 | # |
---|
848 | # |
---|
849 | [binned-binsize-3000-posterior-lv-H3K27me3-BN-male-bio2-merged-offset-0-posterior] |
---|
850 | feature = microarray_oligo:lv-H3K27me3-BN-male-bio2-merged-offset-0-hmm-posterior-binsize-3000 |
---|
851 | database = histones_h3k27me3 |
---|
852 | glyph = wiggle_xyplot |
---|
853 | smoothing = none |
---|
854 | autoscale = global |
---|
855 | bicolor_pivot = 0.99 |
---|
856 | pos_color = red |
---|
857 | neg_color = gray |
---|
858 | height = 25 |
---|
859 | graph_type = boxes |
---|
860 | scale = right |
---|
861 | description = 1 |
---|
862 | category = Binned H3k27me3 data |
---|
863 | key = lv-H3K27me3-BN-male-bio2-merged-offset-0-hmm-posterior-binsize-3000 |
---|
864 | |
---|
865 | |
---|
866 | #include "/project/intranet/gbrowse2/databases/rn4/histone-modifications/binned-data/binned-data.conf" |
---|
867 | |
---|
868 | |
---|
869 | ############################################################################### |
---|
870 | ### microrna track configurations |
---|
871 | |
---|
872 | [Coverage-BN-mirna] |
---|
873 | feature = coverage |
---|
874 | glyph = wiggle_xyplot |
---|
875 | database = BN-mirna |
---|
876 | height = 50 |
---|
877 | fgcolor = black |
---|
878 | bgcolor = indigo |
---|
879 | key = Coverage BN mirna |
---|
880 | category = microRNA |
---|
881 | label = 0 # Labels on wiggle tracks are redundant. |
---|
882 | |
---|
883 | [Reads-BN-mirna] |
---|
884 | feature = match |
---|
885 | glyph = segments |
---|
886 | draw_target = 1 |
---|
887 | show_mismatch = 1 |
---|
888 | mismatch_color = red |
---|
889 | database = BN-mirna |
---|
890 | bgcolor = blue |
---|
891 | fgcolor = blue |
---|
892 | height = 5 |
---|
893 | label density = 50 |
---|
894 | bump = fast |
---|
895 | key = Reads BN mirna |
---|
896 | category = microRNA |
---|
897 | |
---|
898 | #[Coverage-HXB01-mirna] |
---|
899 | #feature = coverage |
---|
900 | #glyph = wiggle_xyplot |
---|
901 | #database = HXB01-mirna |
---|
902 | #height = 50 |
---|
903 | #fgcolor = black |
---|
904 | #bgcolor = indigo |
---|
905 | #key = Coverage HXB01 mirna |
---|
906 | #category = microRNA |
---|
907 | #label = 0 |
---|
908 | # |
---|
909 | #[Reads-HXB01-mirna] |
---|
910 | #feature = match |
---|
911 | #glyph = segments |
---|
912 | #draw_target = 1 |
---|
913 | #show_mismatch = 1 |
---|
914 | #mismatch_color = red |
---|
915 | #database = HXB01-mirna |
---|
916 | #bgcolor = blue |
---|
917 | #fgcolor = blue |
---|
918 | #height = 5 |
---|
919 | #label density = 50 |
---|
920 | #bump = fast |
---|
921 | #key = Reads HXB01 mirna |
---|
922 | #category = microRNA |
---|
923 | # |
---|
924 | #[Coverage-HXB03-mirna] |
---|
925 | #feature = coverage |
---|
926 | #glyph = wiggle_xyplot |
---|
927 | #database = HXB03-mirna |
---|
928 | #height = 50 |
---|
929 | #fgcolor = black |
---|
930 | #bgcolor = indigo |
---|
931 | #key = Coverage HXB03 mirna |
---|
932 | #category = microRNA |
---|
933 | #label = 0 |
---|
934 | # |
---|
935 | #[Reads-HXB03-mirna] |
---|
936 | #feature = match |
---|
937 | #glyph = segments |
---|
938 | #draw_target = 1 |
---|
939 | #show_mismatch = 1 |
---|
940 | #mismatch_color = red |
---|
941 | #database = HXB03-mirna |
---|
942 | #bgcolor = blue |
---|
943 | #fgcolor = blue |
---|
944 | #height = 5 |
---|
945 | #label density = 50 |
---|
946 | #bump = fast |
---|
947 | #key = Reads HXB03 mirna |
---|
948 | #category = microRNA |
---|
949 | # |
---|
950 | #[Coverage-HXB05-mirna] |
---|
951 | #feature = coverage |
---|
952 | #glyph = wiggle_xyplot |
---|
953 | #database = HXB05-mirna |
---|
954 | #height = 50 |
---|
955 | #fgcolor = black |
---|
956 | #bgcolor = indigo |
---|
957 | #key = Coverage HXB05 mirna |
---|
958 | #category = microRNA |
---|
959 | #label = 0 |
---|
960 | # |
---|
961 | #[Reads-HXB05-mirna] |
---|
962 | #feature = match |
---|
963 | #glyph = segments |
---|
964 | #draw_target = 1 |
---|
965 | #show_mismatch = 1 |
---|
966 | #mismatch_color = red |
---|
967 | #database = HXB05-mirna |
---|
968 | #bgcolor = blue |
---|
969 | #fgcolor = blue |
---|
970 | #height = 5 |
---|
971 | #label density = 50 |
---|
972 | #bump = fast |
---|
973 | #key = Reads HXB05 mirna |
---|
974 | #category = microRNA |
---|
975 | # |
---|
976 | #[Coverage-HXB10-mirna] |
---|
977 | #feature = coverage |
---|
978 | #glyph = wiggle_xyplot |
---|
979 | #database = HXB10-mirna |
---|
980 | #height = 50 |
---|
981 | #fgcolor = black |
---|
982 | #bgcolor = indigo |
---|
983 | #key = Coverage HXB10 mirna |
---|
984 | #category = microRNA |
---|
985 | #label = 0 |
---|
986 | # |
---|
987 | #[Reads-HXB10-mirna] |
---|
988 | #feature = match |
---|
989 | #glyph = segments |
---|
990 | #draw_target = 1 |
---|
991 | #show_mismatch = 1 |
---|
992 | #mismatch_color = red |
---|
993 | #database = HXB10-mirna |
---|
994 | #bgcolor = blue |
---|
995 | #fgcolor = blue |
---|
996 | #height = 5 |
---|
997 | #label density = 50 |
---|
998 | #bump = fast |
---|
999 | #key = Reads HXB10 mirna |
---|
1000 | #category = microRNA |
---|
1001 | # |
---|
1002 | #[Coverage-HXB15-mirna] |
---|
1003 | #feature = coverage |
---|
1004 | #glyph = wiggle_xyplot |
---|
1005 | #database = HXB15-mirna |
---|
1006 | #height = 50 |
---|
1007 | #fgcolor = black |
---|
1008 | #bgcolor = indigo |
---|
1009 | #key = Coverage HXB15 mirna |
---|
1010 | #category = microRNA |
---|
1011 | #label = 0 |
---|
1012 | # |
---|
1013 | #[Reads-HXB15-mirna] |
---|
1014 | #feature = match |
---|
1015 | #glyph = segments |
---|
1016 | #draw_target = 1 |
---|
1017 | #show_mismatch = 1 |
---|
1018 | #mismatch_color = red |
---|
1019 | #database = HXB15-mirna |
---|
1020 | #bgcolor = blue |
---|
1021 | #fgcolor = blue |
---|
1022 | #height = 5 |
---|
1023 | #label density = 50 |
---|
1024 | #bump = fast |
---|
1025 | #key = Reads HXB15 mirna |
---|
1026 | #category = microRNA |
---|
1027 | # |
---|
1028 | #[Coverage-HXB18-mirna] |
---|
1029 | #feature = coverage |
---|
1030 | #glyph = wiggle_xyplot |
---|
1031 | #database = HXB18-mirna |
---|
1032 | #height = 50 |
---|
1033 | #fgcolor = black |
---|
1034 | #bgcolor = indigo |
---|
1035 | #key = Coverage HXB18 mirna |
---|
1036 | #category = microRNA |
---|
1037 | #label = 0 |
---|
1038 | # |
---|
1039 | #[Reads-HXB18-mirna] |
---|
1040 | #feature = match |
---|
1041 | #glyph = segments |
---|
1042 | #draw_target = 1 |
---|
1043 | #show_mismatch = 1 |
---|
1044 | #mismatch_color = red |
---|
1045 | #database = HXB18-mirna |
---|
1046 | #bgcolor = blue |
---|
1047 | #fgcolor = blue |
---|
1048 | #height = 5 |
---|
1049 | #label density = 50 |
---|
1050 | #bump = fast |
---|
1051 | #key = Reads HXB18 mirna |
---|
1052 | #category = microRNA |
---|
1053 | # |
---|
1054 | #[Coverage-HXB21-mirna] |
---|
1055 | #feature = coverage |
---|
1056 | #glyph = wiggle_xyplot |
---|
1057 | #database = HXB21-mirna |
---|
1058 | #height = 50 |
---|
1059 | #fgcolor = black |
---|
1060 | #bgcolor = indigo |
---|
1061 | #key = Coverage HXB21 mirna |
---|
1062 | #category = microRNA |
---|
1063 | #label = 0 |
---|
1064 | # |
---|
1065 | #[Reads-HXB21-mirna] |
---|
1066 | #feature = match |
---|
1067 | #glyph = segments |
---|
1068 | #draw_target = 1 |
---|
1069 | #show_mismatch = 1 |
---|
1070 | #mismatch_color = red |
---|
1071 | #database = HXB21-mirna |
---|
1072 | #bgcolor = blue |
---|
1073 | #fgcolor = blue |
---|
1074 | #height = 5 |
---|
1075 | #label density = 50 |
---|
1076 | #bump = fast |
---|
1077 | #key = Reads HXB21 mirna |
---|
1078 | #category = microRNA |
---|
1079 | # |
---|
1080 | #[Coverage-HXB23-mirna] |
---|
1081 | #feature = coverage |
---|
1082 | #glyph = wiggle_xyplot |
---|
1083 | #database = HXB23-mirna |
---|
1084 | #height = 50 |
---|
1085 | #fgcolor = black |
---|
1086 | #bgcolor = indigo |
---|
1087 | #key = Coverage HXB23 mirna |
---|
1088 | #category = microRNA |
---|
1089 | #label = 0 |
---|
1090 | # |
---|
1091 | #[Reads-HXB23-mirna] |
---|
1092 | #feature = match |
---|
1093 | #glyph = segments |
---|
1094 | #draw_target = 1 |
---|
1095 | #show_mismatch = 1 |
---|
1096 | #mismatch_color = red |
---|
1097 | #database = HXB23-mirna |
---|
1098 | #bgcolor = blue |
---|
1099 | #fgcolor = blue |
---|
1100 | #height = 5 |
---|
1101 | #label density = 50 |
---|
1102 | #bump = fast |
---|
1103 | #key = Reads HXB23 mirna |
---|
1104 | #category = microRNA |
---|
1105 | # |
---|
1106 | #[Coverage-HXB25-mirna] |
---|
1107 | #feature = coverage |
---|
1108 | #glyph = wiggle_xyplot |
---|
1109 | #database = HXB25-mirna |
---|
1110 | #height = 50 |
---|
1111 | #fgcolor = black |
---|
1112 | #bgcolor = indigo |
---|
1113 | #key = Coverage HXB25 mirna |
---|
1114 | #category = microRNA |
---|
1115 | #label = 0 |
---|
1116 | # |
---|
1117 | #[Reads-HXB25-mirna] |
---|
1118 | #feature = match |
---|
1119 | #glyph = segments |
---|
1120 | #draw_target = 1 |
---|
1121 | #show_mismatch = 1 |
---|
1122 | #mismatch_color = red |
---|
1123 | #database = HXB25-mirna |
---|
1124 | #bgcolor = blue |
---|
1125 | #fgcolor = blue |
---|
1126 | #height = 5 |
---|
1127 | #label density = 50 |
---|
1128 | #bump = fast |
---|
1129 | #key = Reads HXB25 mirna |
---|
1130 | #category = microRNA |
---|
1131 | # |
---|
1132 | #[Coverage-HXB29-mirna] |
---|
1133 | #feature = coverage |
---|
1134 | #glyph = wiggle_xyplot |
---|
1135 | #database = HXB29-mirna |
---|
1136 | #height = 50 |
---|
1137 | #fgcolor = black |
---|
1138 | #bgcolor = indigo |
---|
1139 | #key = Coverage HXB29 mirna |
---|
1140 | #category = microRNA |
---|
1141 | #label = 0 |
---|
1142 | # |
---|
1143 | #[Reads-HXB29-mirna] |
---|
1144 | #feature = match |
---|
1145 | #glyph = segments |
---|
1146 | #draw_target = 1 |
---|
1147 | #show_mismatch = 1 |
---|
1148 | #mismatch_color = red |
---|
1149 | #database = HXB29-mirna |
---|
1150 | #bgcolor = blue |
---|
1151 | #fgcolor = blue |
---|
1152 | #height = 5 |
---|
1153 | #label density = 50 |
---|
1154 | #bump = fast |
---|
1155 | #key = Reads HXB29 mirna |
---|
1156 | #category = microRNA |
---|
1157 | # |
---|
1158 | #[Coverage-SHR-mirna] |
---|
1159 | #feature = coverage |
---|
1160 | #glyph = wiggle_xyplot |
---|
1161 | #database = SHR-mirna |
---|
1162 | #height = 50 |
---|
1163 | #fgcolor = black |
---|
1164 | #bgcolor = indigo |
---|
1165 | #key = Coverage SHR mirna |
---|
1166 | #category = microRNA |
---|
1167 | #label = 0 |
---|
1168 | # |
---|
1169 | #[Reads-SHR-mirna] |
---|
1170 | #feature = match |
---|
1171 | #glyph = segments |
---|
1172 | #draw_target = 1 |
---|
1173 | #show_mismatch = 1 |
---|
1174 | #mismatch_color = red |
---|
1175 | #database = SHR-mirna |
---|
1176 | #bgcolor = blue |
---|
1177 | #fgcolor = blue |
---|
1178 | #height = 5 |
---|
1179 | #label density = 50 |
---|
1180 | #bump = fast |
---|
1181 | #key = Reads SHR mirna |
---|
1182 | #category = microRNA |
---|
1183 | |
---|
1184 | |
---|
1185 | |
---|
1186 | ############################################################################### |
---|
1187 | ### Rbm20 track configurations |
---|
1188 | |
---|
1189 | #[Coverage-rbm20-mutant] |
---|
1190 | #feature = coverage |
---|
1191 | #glyph = wiggle_xyplot |
---|
1192 | #database = rbm20-mutant |
---|
1193 | #height = 50 |
---|
1194 | #fgcolor = black |
---|
1195 | #bgcolor = indigo |
---|
1196 | #key = Coverage Rbm 20 mutant |
---|
1197 | #category = Rbm20 mRNA |
---|
1198 | #label = 0 |
---|
1199 | # |
---|
1200 | #[Reads-rbm20-mutant] |
---|
1201 | #feature = match |
---|
1202 | #glyph = segments |
---|
1203 | #draw_target = 1 |
---|
1204 | #show_mismatch = 1 |
---|
1205 | #mismatch_color = red |
---|
1206 | #database = rbm20-mutant |
---|
1207 | #bgcolor = blue |
---|
1208 | #fgcolor = blue |
---|
1209 | #height = 5 |
---|
1210 | #label density = 50 |
---|
1211 | #bump = fast |
---|
1212 | #key = Reads Rbm 20 mutant |
---|
1213 | #category = Rbm20 mRNA |
---|
1214 | # |
---|
1215 | [Coverage-rbm20-wildtype] |
---|
1216 | feature = coverage |
---|
1217 | glyph = wiggle_xyplot |
---|
1218 | database = rbm20-wildtype |
---|
1219 | height = 50 |
---|
1220 | fgcolor = black |
---|
1221 | bgcolor = indigo |
---|
1222 | key = Coverage BN |
---|
1223 | category = mRNA |
---|
1224 | label = 0 |
---|
1225 | |
---|
1226 | [Reads-rbm20-wildtype] |
---|
1227 | feature = match |
---|
1228 | glyph = segments |
---|
1229 | draw_target = 1 |
---|
1230 | show_mismatch = 1 |
---|
1231 | mismatch_color = red |
---|
1232 | database = rbm20-wildtype |
---|
1233 | bgcolor = blue |
---|
1234 | fgcolor = blue |
---|
1235 | height = 5 |
---|
1236 | label density = 50 |
---|
1237 | bump = fast |
---|
1238 | key = Reads BN |
---|
1239 | category = mRNA |
---|
1240 | |
---|
1241 | [Reads-rbm20-wildtype-pairs] |
---|
1242 | feature = read_pair |
---|
1243 | glyph = segments |
---|
1244 | database = rbm20-wildtype |
---|
1245 | draw_target = 1 |
---|
1246 | show_mismatch = 1 |
---|
1247 | bgcolor = sub { |
---|
1248 | my $f = shift; |
---|
1249 | return $f->attributes('M_UNMAPPED') ? 'red' : 'green'; |
---|
1250 | } |
---|
1251 | fgcolor = green |
---|
1252 | height = 3 |
---|
1253 | label = sub {shift->display_name} |
---|
1254 | label density = 50 |
---|
1255 | bump = fast |
---|
1256 | connector = dashed |
---|
1257 | balloon hover = sub { |
---|
1258 | my $f = shift; |
---|
1259 | return '' unless $f->type eq 'match'; |
---|
1260 | return 'Read: '.$f->display_name.' : '.$f->flag_str; |
---|
1261 | } |
---|
1262 | key = Read Pairs BN |
---|
1263 | category = mRNA |
---|
1264 | |
---|
1265 | [rbm20_cluster] |
---|
1266 | feature = experimental_feature:rbm20_clusters |
---|
1267 | database = rbm20_cluster |
---|
1268 | glyph = generic |
---|
1269 | bgcolor = blue |
---|
1270 | fgcolor = blue |
---|
1271 | forwardcolor = blue |
---|
1272 | reversecolor = blue |
---|
1273 | key = Rbm20 cluster from human HEK cells |
---|
1274 | category = Rbm20 |
---|
1275 | |
---|
1276 | [rbm20_cufflinks_genes] |
---|
1277 | database = rbm20_cluster |
---|
1278 | feature = gene:Cufflinks |
---|
1279 | glyph = gene |
---|
1280 | bgcolor = dodgerblue |
---|
1281 | forwardcolor = dodgerblue |
---|
1282 | reversecolor = turquoise |
---|
1283 | label = sub { my $f = shift; |
---|
1284 | my $name = $f->display_name; |
---|
1285 | my @aliases = sort $f->attributes('Alias'); |
---|
1286 | $name .= " (@aliases)" if @aliases; |
---|
1287 | $name; |
---|
1288 | } |
---|
1289 | height = 6 |
---|
1290 | description = 0 |
---|
1291 | key = Cufflinks genes |
---|
1292 | category = Rbm20 |
---|
1293 | |
---|
1294 | |
---|
1295 | # |
---|
1296 | # |
---|
1297 | #[Coverage-rbm20-mutant-fwd] |
---|
1298 | #feature = coverage |
---|
1299 | #glyph = wiggle_xyplot |
---|
1300 | #database = rbm20-mutant-fwd |
---|
1301 | #height = 50 |
---|
1302 | #fgcolor = black |
---|
1303 | #bgcolor = indigo |
---|
1304 | #key = Coverage Rbm 20 mutant fwd |
---|
1305 | #category = Rbm20 mRNA |
---|
1306 | #label = 0 |
---|
1307 | # |
---|
1308 | #[Reads-rbm20-mutant-fwd] |
---|
1309 | #feature = match |
---|
1310 | #glyph = segments |
---|
1311 | #draw_target = 1 |
---|
1312 | #show_mismatch = 1 |
---|
1313 | #mismatch_color = red |
---|
1314 | #database = rbm20-mutant-fwd |
---|
1315 | #bgcolor = blue |
---|
1316 | #fgcolor = blue |
---|
1317 | #height = 5 |
---|
1318 | #label density = 50 |
---|
1319 | #bump = fast |
---|
1320 | #key = Reads Rbm 20 mutant fwd |
---|
1321 | #category = Rbm20 mRNA |
---|
1322 | # |
---|
1323 | #[Coverage-rbm20-wildtype-rev] |
---|
1324 | #feature = coverage |
---|
1325 | #glyph = wiggle_xyplot |
---|
1326 | #database = rbm20-wildtype-rev |
---|
1327 | #height = 50 |
---|
1328 | #fgcolor = black |
---|
1329 | #bgcolor = indigo |
---|
1330 | #key = Coverage Rbm 20 wildtype rev |
---|
1331 | #category = Rbm20 mRNA |
---|
1332 | #label = 0 |
---|
1333 | # |
---|
1334 | #[Reads-rbm20-wildtype-rev] |
---|
1335 | #feature = match |
---|
1336 | #glyph = segments |
---|
1337 | #draw_target = 1 |
---|
1338 | #show_mismatch = 1 |
---|
1339 | #mismatch_color = red |
---|
1340 | #database = rbm20-wildtype-rev |
---|
1341 | #bgcolor = blue |
---|
1342 | #fgcolor = blue |
---|
1343 | #height = 5 |
---|
1344 | #label density = 50 |
---|
1345 | #bump = fast |
---|
1346 | #key = Reads Rbm 20 wildtype rev |
---|
1347 | #category = Rbm20 mRNA |
---|
1348 | |
---|
1349 | |
---|
1350 | #[Coverage-wildtype2] |
---|
1351 | #feature = solid:wildtype2-s14 |
---|
1352 | #glyph = wiggle_xyplot |
---|
1353 | #database = rbm20 |
---|
1354 | #height = 50 |
---|
1355 | #fgcolor = black |
---|
1356 | #bgcolor = indigo |
---|
1357 | #key = Coverage wildtype 2 |
---|
1358 | #category = Rbm20 mRNA-seq |
---|
1359 | #label = 0 |
---|
1360 | |
---|
1361 | |
---|
1362 | |
---|
1363 | ############################################################################### |
---|
1364 | ### Annotation track configurations |
---|
1365 | |
---|
1366 | |
---|
1367 | # microrna genes |
---|
1368 | [mirna-genes] |
---|
1369 | feature = miRNA |
---|
1370 | database = scaffolds |
---|
1371 | glyph = generic |
---|
1372 | bgcolor = red |
---|
1373 | forwardcolor = red |
---|
1374 | reversecolor = red |
---|
1375 | key = mirbase microRNA |
---|
1376 | category = microRNA |
---|
1377 | |
---|
1378 | |
---|
1379 | |
---|
1380 | # view deletions and snps |
---|
1381 | |
---|
1382 | [shr-deletions] |
---|
1383 | feature = deletion:SHR |
---|
1384 | database = variations |
---|
1385 | glyph = generic |
---|
1386 | bgcolor = red |
---|
1387 | forwardcolor = red |
---|
1388 | reversecolor = red |
---|
1389 | key = SHR deletion |
---|
1390 | category = Variations |
---|
1391 | |
---|
1392 | |
---|
1393 | [shr-SNPs] |
---|
1394 | feature = SNP:SHR |
---|
1395 | database = variations |
---|
1396 | glyph = triangle |
---|
1397 | point = 1 |
---|
1398 | orient = N |
---|
1399 | height = 6 |
---|
1400 | bgcolor = blue |
---|
1401 | fgcolor = blue |
---|
1402 | key = SHR SNPs |
---|
1403 | category = Variations |
---|
1404 | bump density = 1 |
---|
1405 | |
---|
1406 | #[shr-SNPs:100000] |
---|
1407 | #database = variations |
---|
1408 | #feature = snp_density |
---|
1409 | #glyph = xyplot |
---|
1410 | #graph_type = boxes |
---|
1411 | #scale = right |
---|
1412 | |
---|
1413 | [hxb-sdp] |
---|
1414 | feature = experimental_feature:hxb_sdp |
---|
1415 | database = variations |
---|
1416 | glyph = generic |
---|
1417 | bgcolor = blue |
---|
1418 | fgcolor = blue |
---|
1419 | forwardcolor = blue |
---|
1420 | reversecolor = blue |
---|
1421 | key = BXH/HXB SDPs |
---|
1422 | category = Variations |
---|
1423 | balloon click = <h2>Marker $name</h2> |
---|
1424 | <a href='http://vm7.target.rug.nl/xqtl_unstable/api/find/org.molgenis.xgap.Marker?name=$id'>Marker info from molgenis</a><br> |
---|
1425 | |
---|
1426 | |
---|
1427 | ### |
---|
1428 | ### This is a query by name: |
---|
1429 | ### .../api/find/org.molgenis.xgap.Marker?name=1 |
---|
1430 | |
---|
1431 | |
---|
1432 | [GC:region] |
---|
1433 | glyph = dna |
---|
1434 | global feature = 1 |
---|
1435 | database = scaffolds |
---|
1436 | height = 40 |
---|
1437 | gc_window = auto |
---|
1438 | do_gc = 1 |
---|
1439 | strand = both |
---|
1440 | fgcolor = red |
---|
1441 | axis_color = blue |
---|
1442 | key = GC Content |
---|
1443 | |
---|
1444 | [Genes] |
---|
1445 | feature = gene:protein_coding |
---|
1446 | glyph = gene |
---|
1447 | bgcolor = dodgerblue |
---|
1448 | forwardcolor = dodgerblue |
---|
1449 | reversecolor = turquoise |
---|
1450 | label = sub { my $f = shift; |
---|
1451 | my $name = $f->display_name; |
---|
1452 | my @aliases = sort $f->attributes('Alias'); |
---|
1453 | $name .= " (@aliases)" if @aliases; |
---|
1454 | $name; |
---|
1455 | } |
---|
1456 | height = 6 |
---|
1457 | description = 0 |
---|
1458 | key = Ensembl genes |
---|
1459 | |
---|
1460 | |
---|
1461 | [Translation] |
---|
1462 | glyph = translation |
---|
1463 | global feature = 1 |
---|
1464 | database = scaffolds |
---|
1465 | height = 40 |
---|
1466 | fgcolor = purple |
---|
1467 | strand = +1 |
---|
1468 | translation = 6frame |
---|
1469 | key = 6-frame translation |
---|
1470 | |
---|
1471 | [TranslationF] |
---|
1472 | glyph = translation |
---|
1473 | global feature = 1 |
---|
1474 | database = scaffolds |
---|
1475 | height = 20 |
---|
1476 | fgcolor = purple |
---|
1477 | strand = +1 |
---|
1478 | translation = 3frame |
---|
1479 | key = 3-frame translation (forward) |
---|
1480 | |
---|
1481 | [DNA/GC Content] |
---|
1482 | glyph = dna |
---|
1483 | global feature = 1 |
---|
1484 | database = scaffolds |
---|
1485 | height = 40 |
---|
1486 | do_gc = 1 |
---|
1487 | gc_window = auto |
---|
1488 | strand = both |
---|
1489 | fgcolor = red |
---|
1490 | axis_color = blue |
---|
1491 | |
---|
1492 | [TranslationR] |
---|
1493 | glyph = translation |
---|
1494 | global feature = 1 |
---|
1495 | database = scaffolds |
---|
1496 | height = 20 |
---|
1497 | fgcolor = blue |
---|
1498 | strand = -1 |
---|
1499 | translation = 3frame |
---|
1500 | key = 3-frame translation (reverse) |
---|