[GENERAL]
description = Rattus norvegicus
database = scaffolds
initial landmark = chr19:143000..180000
default tracks = Genes
# examples to show in the introduction
examples = chr1
chr1:80,000..120,000
# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone ID
# try to configure the rubberband menu to query for eQTLs
[DETAIL SELECT MENU]
width = 250
html =
###
### The last entry in the menu list is a molgenis example which creates urls:
### .../api/find/org.molgenis.xgap.Marker?name=chr1:3790000..4759999
#################################
# database definitions
#################################
[scaffolds:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor DBI::mysql
-dsn dbi:mysql:database=rn4
-user apache
[variations:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor DBI::mysql
-dsn dbi:mysql:database=rn4_variations
-user apache
# for the SNP density plots
aggregators = snp_density{bin:SNP:SHR}
###############################################################################
### Rbm 20 databasese
[rbm20_cluster:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor DBI::mysql
-dsn dbi:mysql:database=rn4_rbm20_cluster
-user apache
# [rbm20:database]
# db_adaptor = Bio::DB::SeqFeature::Store
# db_args = -adaptor DBI::mysql
# -dsn dbi:mysql:database=rn4_rbm20
# -user apache
#[rbm20-mutant:database]
#db_adaptor = Bio::DB::Sam
#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
# -bam /var/www/html/gbrowse2/databases/rn4/rbm20/rawreadsmutant-bowtie-sorted.bam.bam
#search options = default
#
[rbm20-wildtype:database]
db_adaptor = Bio::DB::Sam
db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
-bam /var/www/html/gbrowse2/databases/rn4/rbm20/wildtype.bam
search options = default
#[rbm20-mutant-fwd:database]
#db_adaptor = Bio::DB::Sam
#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
# -bam /var/www/html/gbrowse2/databases/rn4/rbm20/rawreadsmutant-bowtie-sorted.bam.bam
#search options = default
#
#[rbm20-wildtype-fwd:database]
#db_adaptor = Bio::DB::Sam
#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
# -bam /var/www/html/gbrowse2/databases/rn4/rbm20/rawreadswildtype-bowtie-sorted.bam.bam
#search options = default
#
#[rbm20-mutant-rev:database]
#db_adaptor = Bio::DB::Sam
#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
# -bam /var/www/html/gbrowse2/databases/rn4/rbm20/rawreadsmutant-bowtie-sorted.bam.bam
#search options = default
#
#[rbm20-wildtype-rev:database]
#db_adaptor = Bio::DB::Sam
#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
# -bam /var/www/html/gbrowse2/databases/rn4/rbm20/rawreadswildtype-bowtie-sorted.bam.bam
#search options = default
###############################################################################
### histone modification databases
[histones:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor DBI::mysql
-dsn dbi:mysql:database=rn4_histones
-user apache
[histones_h3k27me3:database]
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor DBI::mysql
-dsn dbi:mysql:database=rn4_histones_h3k27me3
-user apache
#
[lv-H3K4me3-BN-male-bio2-tech1:database]
db_adaptor = Bio::DB::Sam
db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
-bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K4me3-BN-male-bio2-tech1-rmdup.bam
[lv-H3K4me3-SHR-male-bio2-tech1:database]
db_adaptor = Bio::DB::Sam
db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
-bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K4me3-SHR-male-bio2-tech1-rmdup.bam
[lv-H3K4me3-BN-female-bio1-tech1:database]
db_adaptor = Bio::DB::Sam
db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
-bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K4me3-BN-female-bio1-tech1-rmdup.bam
[lv-H3K4me3-SHR-female-bio1-tech1:database]
db_adaptor = Bio::DB::Sam
db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
-bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K4me3-SHR-female-bio1-tech1-rmdup.bam
[lv-H3K27me3-BN-male-bio2-merged:database]
db_adaptor = Bio::DB::Sam
db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
-bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K27me3-BN-male-bio2-merged.bam
[lv-H3K27me3-BN-male-bio3-merged:database]
db_adaptor = Bio::DB::Sam
db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
-bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K27me3-BN-male-bio3-merged.bam
[lv-H3K27me3-BN-male-bio4-merged:database]
db_adaptor = Bio::DB::Sam
db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
-bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/lv-H3K27me3-BN-male-bio4-merged.bam
[BN-H3K4me3:database]
db_adaptor = Bio::DB::Sam
db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
-bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/BN-H3K4me3-sorted.bam
search options = default
[BN-H3K27me3:database]
db_adaptor = Bio::DB::Sam
db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
-bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/BN-H3K27me3-sorted.bam
search options = default
[BN-input:database]
db_adaptor = Bio::DB::Sam
db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
-bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/BN-input-sorted.bam
search options = default
[SHR-H3K4me3:database]
db_adaptor = Bio::DB::Sam
db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
-bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/SHR-H3K4me3-sorted.bam
search options = default
[SHR-H3K27me3:database]
db_adaptor = Bio::DB::Sam
db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
-bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/SHR-H3K27me3-sorted.bam
search options = default
[SHR-input:database]
db_adaptor = Bio::DB::Sam
db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
-bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/SHR-input-sorted.bam
search options = default
[BXH12-H3K4:database]
db_adaptor = Bio::DB::Sam
db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
-bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/K4-BXH12_sorted.bam
search options = default
[BXH02-H3K4:database]
db_adaptor = Bio::DB::Sam
db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
-bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/K4-BXH02_sorted.bam
search options = default
[BXH03-H3K4:database]
db_adaptor = Bio::DB::Sam
db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
-bam /var/www/html/gbrowse2/databases/rn4/histone-modifications/K4-BXH03.bam
search options = default
###############################################################################
### micro rna databases
[BN-mirna:database]
db_adaptor = Bio::DB::Sam
db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
-bam /var/www/html/gbrowse2/databases/rn4/mirna/BN.csfasta__sorted.bam
search options = default
#[HXB01-mirna:database]
#db_adaptor = Bio::DB::Sam
#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
#-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB01.csfasta__sorted.bam
#search options = default
#[HXB03-mirna:database]
#db_adaptor = Bio::DB::Sam
#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
#-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB03.csfasta__sorted.bam
#search options = default
#[HXB05-mirna:database]
#db_adaptor = Bio::DB::Sam
#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
#-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB05.csfasta__sorted.bam
#search options = default
#[HXB10-mirna:database]
#db_adaptor = Bio::DB::Sam
#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
#-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB10.csfasta__sorted.bam
#search options = default
#[HXB15-mirna:database]
#db_adaptor = Bio::DB::Sam
#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
#-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB15.csfasta__sorted.bam
#search options = default
#[HXB18-mirna:database]
#db_adaptor = Bio::DB::Sam
#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
#-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB18.csfasta__sorted.bam
#search options = default
#[HXB21-mirna:database]
#db_adaptor = Bio::DB::Sam
#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
#-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB21.csfasta__sorted.bam
#search options = default
#[HXB23-mirna:database]
#db_adaptor = Bio::DB::Sam
#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
#-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB23.csfasta__sorted.bam
#search options = default
#[HXB25-mirna:database]
#db_adaptor = Bio::DB::Sam
#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
#-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB25.csfasta__sorted.bam
#search options = default
#[HXB29-mirna:database]
#db_adaptor = Bio::DB::Sam
#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
#-bam /var/www/html/gbrowse2/databases/rn4/mirna/HXB29.csfasta__sorted.bam
#search options = default
#[SHR-mirna:database]
#db_adaptor = Bio::DB::Sam
#db_args = -fasta /var/www/html/gbrowse2/databases/rn4/fasta/Rattus_norvegicus.RGSC3.4.56.dna.toplevel.fa
#-bam /var/www/html/gbrowse2/databases/rn4/mirna/SHR.csfasta__sorted.bam
#search options = default
###############################################################################
### track configurations
# Default glyph settings
[TRACK DEFAULTS]
glyph = generic
database = scaffolds
height = 8
bgcolor = cyan
fgcolor = black
label density = 25
bump density = 100
### TRACK CONFIGURATION ####
# the remainder of the sections configure individual tracks
# view the reads
###############################################################################
### histone modifications track configurations
# for the sex specific analysis
[Coverage-lv-H3K4me3-BN-female-bio1-tech1]
feature = coverage
glyph = wiggle_xyplot
database = lv-H3K4me3-BN-female-bio1-tech1
height = 50
fgcolor = black
bgcolor = indigo
key = Coverage lv-H3K4me3-BN-female-bio1-tech1
category = Histone modifications
label = 0 # Labels on wiggle tracks are redundant.
[Coverage-lv-H3K4me3-SHR-female-bio1-tech1]
feature = coverage
glyph = wiggle_xyplot
database = lv-H3K4me3-SHR-female-bio1-tech1
height = 50
fgcolor = black
bgcolor = indigo
key = Coverage lv-H3K4me3-SHR-female-bio1-tech1
category = Histone modifications
label = 0 # Labels on wiggle tracks are redundant.
[lv-H3K4me3-BN-male-bio2-tech1]
feature = coverage
glyph = wiggle_xyplot
database = lv-H3K4me3-BN-male-bio2-tech1
height = 50
fgcolor = black
bgcolor = indigo
key = Coverage lv-H3K4me3-BN-male-bio2-tech1
category = Histone modifications
label = 0 # Labels on wiggle tracks are redundant.
[lv-H3K4me3-SHR-male-bio2-tech1-rmdup]
feature = coverage
glyph = wiggle_xyplot
database = lv-H3K4me3-SHR-male-bio2-tech1
height = 50
fgcolor = black
bgcolor = indigo
key = Coverage lv-H3K4me3-SHR-male-bio2-tech1
category = Histone modifications
label = 0 # Labels on wiggle tracks are redundant.
# BN
[Coverage-lv-H3K27me3-BN-male-bio2-merged]
feature = coverage
glyph = wiggle_xyplot
database = lv-H3K27me3-BN-male-bio2-merged
height = 50
fgcolor = black
bgcolor = indigo
key = Coverage lv-H3K27me3-BN-male-bio2-merged
category = Histone modifications
label = 0 # Labels on wiggle tracks are redundant.
[Coverage-lv-H3K27me3-BN-male-bio3-merged]
feature = coverage
glyph = wiggle_xyplot
database = lv-H3K27me3-BN-male-bio3-merged
height = 50
fgcolor = black
bgcolor = indigo
key = Coverage lv-H3K27me3-BN-male-bio3-merged
category = Histone modifications
label = 0 # Labels on wiggle tracks are redundant.
[Coverage-lv-H3K27me3-BN-male-bio4-merged]
feature = coverage
glyph = wiggle_xyplot
database = lv-H3K27me3-BN-male-bio4-merged
height = 50
fgcolor = black
bgcolor = indigo
key = Coverage lv-H3K27me3-BN-male-bio4-merged
category = Histone modifications
label = 0 # Labels on wiggle tracks are redundant.
[Coverage-BN-H3K4me3]
feature = coverage
glyph = wiggle_xyplot
database = BN-H3K4me3
height = 50
fgcolor = black
bgcolor = indigo
key = Coverage BN-H3K4me3
category = Histone modifications
label = 0 # Labels on wiggle tracks are redundant.
# [Coverage-BN-H3K27me3]
# feature = coverage
# glyph = wiggle_xyplot
# database = BN-H3K27me3
# height = 50
# fgcolor = black
# bgcolor = indigo
# key = Coverage BN-H3K27me3
# category = Histone modifications
# label = 0 # Labels on wiggle tracks are redundant.
[Coverage-BN-input]
feature = coverage
glyph = wiggle_xyplot
database = BN-input
height = 50
fgcolor = black
bgcolor = indigo
key = Coverage BN-input
category = Histone modifications
label = 0 # Labels on wiggle tracks are redundant.
# [Reads-BN-H3K4me3]
# feature = match
# glyph = segments
# draw_target = 1
# show_mismatch = 1
# mismatch_color = red
# database = BN-H3K4me3
# bgcolor = blue
# fgcolor = blue
# height = 5
# label density = 50
# bump = fast
# key = Reads BN-H3K4me3
# category = Histone modifications
#
# [Reads-BN-H3K27me3]
# feature = match
# glyph = segments
# draw_target = 1
# show_mismatch = 1
# mismatch_color = red
# database = BN-H3K27me3
# bgcolor = blue
# fgcolor = blue
# height = 5
# label density = 50
# bump = fast
# key = Reads BN-H3K27me3
# category = Histone modifications
#
# [Reads-BN-input]
# feature = match
# glyph = segments
# draw_target = 1
# show_mismatch = 1
# mismatch_color = red
# database = BN-input
# bgcolor = blue
# fgcolor = blue
# height = 5
# label density = 50
# bump = fast
# key = Reads BN-input
# category = Histone modifications
# SHR reads
[Coverage-SHR-H3K4me3]
feature = coverage
glyph = wiggle_xyplot
database = SHR-H3K4me3
height = 50
fgcolor = black
bgcolor = indigo
key = Coverage SHR-H3K4me3
category = Histone modifications
label = 0 # Labels on wiggle tracks are redundant.
[Coverage-SHR-input]
feature = coverage
glyph = wiggle_xyplot
database = SHR-input
height = 50
fgcolor = black
bgcolor = indigo
key = Coverage SHR-input
category = Histone modifications
label = 0 # Labels on wiggle tracks are redundant.
# [Reads-SHR-H3K4me3]
# feature = match
# glyph = segments
# draw_target = 1
# show_mismatch = 1
# mismatch_color = red
# database = SHR-H3K4me3
# bgcolor = blue
# fgcolor = blue
# height = 5
# label density = 50
# bump = fast
# key = Reads SHR-H3K4me3
# category = Histone modifications
#
# [Reads-SHR-H3K27me3]
# feature = match
# glyph = segments
# draw_target = 1
# show_mismatch = 1
# mismatch_color = red
# database = SHR-H3K27me3
# bgcolor = blue
# fgcolor = blue
# height = 5
# label density = 50
# bump = fast
# key = Reads SHR-H3K27me3
# category = Histone modifications
#
# [Reads-SHR-input]
# feature = match
# glyph = segments
# draw_target = 1
# show_mismatch = 1
# mismatch_color = red
# database = SHR-input
# bgcolor = blue
# fgcolor = blue
# height = 5
# label density = 50
# bump = fast
# key = Reads SHR-input
# category = Histone modifications
#
#
# # reads for the RI strains
# [Coverage-BXH12-H3K4me3]
# feature = coverage
# glyph = wiggle_xyplot
# database = BXH12-H3K4
# height = 50
# fgcolor = black
# bgcolor = indigo
# key = Coverage BXH12-H3K4
# category = Histone modifications
# label = 0 # Labels on wiggle tracks are redundant.
#
# [Reads-BXH12-H3K4me3]
# feature = match
# glyph = segments
# draw_target = 1
# show_mismatch = 1
# mismatch_color = red
# database = BXH12-H3K4
# bgcolor = blue
# fgcolor = blue
# height = 5
# label density = 50
# bump = fast
# key = Reads BXH12-H3K4me3
# category = Histone modifications
#
#
# [Coverage-BXH02-H3K4me3]
# feature = coverage
# glyph = wiggle_xyplot
# database = BXH02-H3K4
# height = 50
# fgcolor = black
# bgcolor = indigo
# key = Coverage BXH102-H3K4
# category = Histone modifications
# label = 0 # Labels on wiggle tracks are redundant.
#
# [Reads-BXH02-H3K4me3]
# feature = match
# glyph = segments
# draw_target = 1
# show_mismatch = 1
# mismatch_color = red
# database = BXH02-H3K4
# bgcolor = blue
# fgcolor = blue
# height = 5
# label density = 50
# bump = fast
# key = Reads BXH02-H3K4me3
# category = Histone modifications
#
# [Coverage-BXH03-H3K4me3]
# feature = coverage
# glyph = wiggle_xyplot
# database = BXH03-H3K4
# height = 50
# fgcolor = black
# bgcolor = indigo
# key = Coverage BXH103-H3K4
# category = Histone modifications
# label = 0 # Labels on wiggle tracks are redundant.
#
#
# [Reads-BXH03-H3K4me3]
# feature = match
# glyph = segments
# draw_target = 1
# show_mismatch = 1
# mismatch_color = red
# database = BXH03-H3K4
# bgcolor = blue
# fgcolor = blue
# height = 5
# label density = 50
# bump = fast
# key = Reads BXH03-H3K4me3
# category = Histone modifications
#
#
# # view the results of the island calling and differential analysis
# [sicer-BN-H3K4me3]
# feature = experimental_feature:sicer-BN-H3K4me3
# database = histones
# glyph = generic
# bgcolor = red
# forwardcolor = red
# reversecolor = red
# key = Sicer BN-H3K4me3
# category = Histone modifications
#
# [sicer-BN-H3K27me3]
# feature = experimental_feature:sicer-BN-H3K27me3
# database = histones
# glyph = generic
# bgcolor = red
# forwardcolor = red
# reversecolor = red
# key = Sicer BN-H3K27me3
# category = Histone modifications
#
# [sicer-BN-input]
# feature = experimental_feature:sicer-BN-input
# database = histones
# glyph = generic
# bgcolor = red
# forwardcolor = red
# reversecolor = red
# key = Sicer BN-input
# category = Histone modifications
#
# [sicer-SHR-H3K4me3]
# feature = experimental_feature:sicer-SHR-H3K4me3
# database = histones
# glyph = generic
# bgcolor = red
# forwardcolor = red
# reversecolor = red
# key = Sicer SHR-H3K4me3
# category = Histone modifications
#
# [sicer-SHR-H3K27me3]
# feature = experimental_feature:sicer-SHR-H3K27me3
# database = histones
# glyph = generic
# bgcolor = red
# forwardcolor = red
# reversecolor = red
# key = Sicer SHR-H3K27me3
# category = Histone modifications
#
# [sicer-SHR-input]
# feature = experimental_feature:sicer-SHR-input
# database = histones
# glyph = generic
# bgcolor = red
# forwardcolor = red
# reversecolor = red
# key = Sicer SHR-input
# category = Histone modifications
#
# [chipdiff-H3K4me3]
# feature = experimental_feature:chipdiff-H3K4me3
# database = histones
# glyph = generic
# bgcolor = red
# forwardcolor = red
# reversecolor = red
# key = Chipdiff H3K4me3
# category = Histone modifications
#
# [chipdiff-H3K27me3]
# feature = experimental_feature:chipdiff-H3K27me3
# database = histones
# glyph = generic
# bgcolor = red
# forwardcolor = red
# reversecolor = red
# key = Chipdiff H3K27me3
# category = Histone modifications
#
#
# # tracks for the peak calls in the RI strains
# [sicer-H3K4-BXH02]
# feature = experimental_feature:sicer-K4-BXH02
# database = histones
# glyph = generic
# bgcolor = red
# forwardcolor = red
# reversecolor = red
# key = Sicer H3K4 BXH02
# category = Histone modifications
#
#
# [sicer-H3K4-BXH12]
# feature = experimental_feature:sicer-K4-BXH12
# database = histones
# glyph = generic
# bgcolor = red
# forwardcolor = red
# reversecolor = red
# key = Sicer H3K4 BXH12
# category = Histone modifications
#
###############################################################################
### Binned H3K27me3 data
# [binned-lv-H3K27me3-BN-male-bio4-merged-offset-3750]
# feature = microarray_oligo:lv-H3K27me3-BN-male-bio4-merged-offset-3750
# database = histones_h3k27me3
# glyph = wiggle_xyplot
# smoothing = none
# autoscale = local
# bgcolor = indigo
# height = 50
# graph_type = boxes
# scale = right
# description = 1
# category = Binned H3k27me3 data
# key = lv-H3K27me3-BN-male-bio4-merged-offset-3750
#
# [posterior-lv-H3K27me3-BN-male-bio4-merged-offset-3750]
# feature = microarray_oligo:lv-H3K27me3-BN-male-bio4-merged-offset-3750-hmm
# database = histones_h3k27me3
# glyph = wiggle_xyplot
# smoothing = none
# autoscale = global
# bicolor_pivot = 0.99
# pos_color = red
# neg_color = gray
# height = 25
# graph_type = boxes
# scale = right
# description = 1
# category = Binned H3k27me3 data
# key = lv-H3K27me3-BN-male-bio4-merged-offset-3750-hmm
#[binned-binsize-5000-posterior-lv-H3K27me3-BN-male-bio2-merged-avg-posterior]
#feature = microarray_oligo:lv-H3K27me3-BN-male-bio2-merged-avg-posterior-binsize-5000
#database = histones_h3k27me3
#glyph = wiggle_xyplot
#smoothing = none
#autoscale = global
#bicolor_pivot = 0.99
#pos_color = red
#neg_color = gray
#height = 25
#graph_type = boxes
#scale = right
#description = 1
#category = Binned H3k27me3 data
#key = lv-H3K27me3-BN-male-bio2-merged-hmm-avg-binsize-5000
#
#
[binned-binsize-3000-posterior-lv-H3K27me3-BN-male-bio2-merged-offset-0-posterior]
feature = microarray_oligo:lv-H3K27me3-BN-male-bio2-merged-offset-0-hmm-posterior-binsize-3000
database = histones_h3k27me3
glyph = wiggle_xyplot
smoothing = none
autoscale = global
bicolor_pivot = 0.99
pos_color = red
neg_color = gray
height = 25
graph_type = boxes
scale = right
description = 1
category = Binned H3k27me3 data
key = lv-H3K27me3-BN-male-bio2-merged-offset-0-hmm-posterior-binsize-3000
#include "/project/intranet/gbrowse2/databases/rn4/histone-modifications/binned-data/binned-data.conf"
###############################################################################
### microrna track configurations
[Coverage-BN-mirna]
feature = coverage
glyph = wiggle_xyplot
database = BN-mirna
height = 50
fgcolor = black
bgcolor = indigo
key = Coverage BN mirna
category = microRNA
label = 0 # Labels on wiggle tracks are redundant.
[Reads-BN-mirna]
feature = match
glyph = segments
draw_target = 1
show_mismatch = 1
mismatch_color = red
database = BN-mirna
bgcolor = blue
fgcolor = blue
height = 5
label density = 50
bump = fast
key = Reads BN mirna
category = microRNA
#[Coverage-HXB01-mirna]
#feature = coverage
#glyph = wiggle_xyplot
#database = HXB01-mirna
#height = 50
#fgcolor = black
#bgcolor = indigo
#key = Coverage HXB01 mirna
#category = microRNA
#label = 0
#
#[Reads-HXB01-mirna]
#feature = match
#glyph = segments
#draw_target = 1
#show_mismatch = 1
#mismatch_color = red
#database = HXB01-mirna
#bgcolor = blue
#fgcolor = blue
#height = 5
#label density = 50
#bump = fast
#key = Reads HXB01 mirna
#category = microRNA
#
#[Coverage-HXB03-mirna]
#feature = coverage
#glyph = wiggle_xyplot
#database = HXB03-mirna
#height = 50
#fgcolor = black
#bgcolor = indigo
#key = Coverage HXB03 mirna
#category = microRNA
#label = 0
#
#[Reads-HXB03-mirna]
#feature = match
#glyph = segments
#draw_target = 1
#show_mismatch = 1
#mismatch_color = red
#database = HXB03-mirna
#bgcolor = blue
#fgcolor = blue
#height = 5
#label density = 50
#bump = fast
#key = Reads HXB03 mirna
#category = microRNA
#
#[Coverage-HXB05-mirna]
#feature = coverage
#glyph = wiggle_xyplot
#database = HXB05-mirna
#height = 50
#fgcolor = black
#bgcolor = indigo
#key = Coverage HXB05 mirna
#category = microRNA
#label = 0
#
#[Reads-HXB05-mirna]
#feature = match
#glyph = segments
#draw_target = 1
#show_mismatch = 1
#mismatch_color = red
#database = HXB05-mirna
#bgcolor = blue
#fgcolor = blue
#height = 5
#label density = 50
#bump = fast
#key = Reads HXB05 mirna
#category = microRNA
#
#[Coverage-HXB10-mirna]
#feature = coverage
#glyph = wiggle_xyplot
#database = HXB10-mirna
#height = 50
#fgcolor = black
#bgcolor = indigo
#key = Coverage HXB10 mirna
#category = microRNA
#label = 0
#
#[Reads-HXB10-mirna]
#feature = match
#glyph = segments
#draw_target = 1
#show_mismatch = 1
#mismatch_color = red
#database = HXB10-mirna
#bgcolor = blue
#fgcolor = blue
#height = 5
#label density = 50
#bump = fast
#key = Reads HXB10 mirna
#category = microRNA
#
#[Coverage-HXB15-mirna]
#feature = coverage
#glyph = wiggle_xyplot
#database = HXB15-mirna
#height = 50
#fgcolor = black
#bgcolor = indigo
#key = Coverage HXB15 mirna
#category = microRNA
#label = 0
#
#[Reads-HXB15-mirna]
#feature = match
#glyph = segments
#draw_target = 1
#show_mismatch = 1
#mismatch_color = red
#database = HXB15-mirna
#bgcolor = blue
#fgcolor = blue
#height = 5
#label density = 50
#bump = fast
#key = Reads HXB15 mirna
#category = microRNA
#
#[Coverage-HXB18-mirna]
#feature = coverage
#glyph = wiggle_xyplot
#database = HXB18-mirna
#height = 50
#fgcolor = black
#bgcolor = indigo
#key = Coverage HXB18 mirna
#category = microRNA
#label = 0
#
#[Reads-HXB18-mirna]
#feature = match
#glyph = segments
#draw_target = 1
#show_mismatch = 1
#mismatch_color = red
#database = HXB18-mirna
#bgcolor = blue
#fgcolor = blue
#height = 5
#label density = 50
#bump = fast
#key = Reads HXB18 mirna
#category = microRNA
#
#[Coverage-HXB21-mirna]
#feature = coverage
#glyph = wiggle_xyplot
#database = HXB21-mirna
#height = 50
#fgcolor = black
#bgcolor = indigo
#key = Coverage HXB21 mirna
#category = microRNA
#label = 0
#
#[Reads-HXB21-mirna]
#feature = match
#glyph = segments
#draw_target = 1
#show_mismatch = 1
#mismatch_color = red
#database = HXB21-mirna
#bgcolor = blue
#fgcolor = blue
#height = 5
#label density = 50
#bump = fast
#key = Reads HXB21 mirna
#category = microRNA
#
#[Coverage-HXB23-mirna]
#feature = coverage
#glyph = wiggle_xyplot
#database = HXB23-mirna
#height = 50
#fgcolor = black
#bgcolor = indigo
#key = Coverage HXB23 mirna
#category = microRNA
#label = 0
#
#[Reads-HXB23-mirna]
#feature = match
#glyph = segments
#draw_target = 1
#show_mismatch = 1
#mismatch_color = red
#database = HXB23-mirna
#bgcolor = blue
#fgcolor = blue
#height = 5
#label density = 50
#bump = fast
#key = Reads HXB23 mirna
#category = microRNA
#
#[Coverage-HXB25-mirna]
#feature = coverage
#glyph = wiggle_xyplot
#database = HXB25-mirna
#height = 50
#fgcolor = black
#bgcolor = indigo
#key = Coverage HXB25 mirna
#category = microRNA
#label = 0
#
#[Reads-HXB25-mirna]
#feature = match
#glyph = segments
#draw_target = 1
#show_mismatch = 1
#mismatch_color = red
#database = HXB25-mirna
#bgcolor = blue
#fgcolor = blue
#height = 5
#label density = 50
#bump = fast
#key = Reads HXB25 mirna
#category = microRNA
#
#[Coverage-HXB29-mirna]
#feature = coverage
#glyph = wiggle_xyplot
#database = HXB29-mirna
#height = 50
#fgcolor = black
#bgcolor = indigo
#key = Coverage HXB29 mirna
#category = microRNA
#label = 0
#
#[Reads-HXB29-mirna]
#feature = match
#glyph = segments
#draw_target = 1
#show_mismatch = 1
#mismatch_color = red
#database = HXB29-mirna
#bgcolor = blue
#fgcolor = blue
#height = 5
#label density = 50
#bump = fast
#key = Reads HXB29 mirna
#category = microRNA
#
#[Coverage-SHR-mirna]
#feature = coverage
#glyph = wiggle_xyplot
#database = SHR-mirna
#height = 50
#fgcolor = black
#bgcolor = indigo
#key = Coverage SHR mirna
#category = microRNA
#label = 0
#
#[Reads-SHR-mirna]
#feature = match
#glyph = segments
#draw_target = 1
#show_mismatch = 1
#mismatch_color = red
#database = SHR-mirna
#bgcolor = blue
#fgcolor = blue
#height = 5
#label density = 50
#bump = fast
#key = Reads SHR mirna
#category = microRNA
###############################################################################
### Rbm20 track configurations
#[Coverage-rbm20-mutant]
#feature = coverage
#glyph = wiggle_xyplot
#database = rbm20-mutant
#height = 50
#fgcolor = black
#bgcolor = indigo
#key = Coverage Rbm 20 mutant
#category = Rbm20 mRNA
#label = 0
#
#[Reads-rbm20-mutant]
#feature = match
#glyph = segments
#draw_target = 1
#show_mismatch = 1
#mismatch_color = red
#database = rbm20-mutant
#bgcolor = blue
#fgcolor = blue
#height = 5
#label density = 50
#bump = fast
#key = Reads Rbm 20 mutant
#category = Rbm20 mRNA
#
[Coverage-rbm20-wildtype]
feature = coverage
glyph = wiggle_xyplot
database = rbm20-wildtype
height = 50
fgcolor = black
bgcolor = indigo
key = Coverage BN
category = mRNA
label = 0
[Reads-rbm20-wildtype]
feature = match
glyph = segments
draw_target = 1
show_mismatch = 1
mismatch_color = red
database = rbm20-wildtype
bgcolor = blue
fgcolor = blue
height = 5
label density = 50
bump = fast
key = Reads BN
category = mRNA
[Reads-rbm20-wildtype-pairs]
feature = read_pair
glyph = segments
database = rbm20-wildtype
draw_target = 1
show_mismatch = 1
bgcolor = sub {
my $f = shift;
return $f->attributes('M_UNMAPPED') ? 'red' : 'green';
}
fgcolor = green
height = 3
label = sub {shift->display_name}
label density = 50
bump = fast
connector = dashed
balloon hover = sub {
my $f = shift;
return '' unless $f->type eq 'match';
return 'Read: '.$f->display_name.' : '.$f->flag_str;
}
key = Read Pairs BN
category = mRNA
[rbm20_cluster]
feature = experimental_feature:rbm20_clusters
database = rbm20_cluster
glyph = generic
bgcolor = blue
fgcolor = blue
forwardcolor = blue
reversecolor = blue
key = Rbm20 cluster from human HEK cells
category = Rbm20
[rbm20_cufflinks_genes]
database = rbm20_cluster
feature = gene:Cufflinks
glyph = gene
bgcolor = dodgerblue
forwardcolor = dodgerblue
reversecolor = turquoise
label = sub { my $f = shift;
my $name = $f->display_name;
my @aliases = sort $f->attributes('Alias');
$name .= " (@aliases)" if @aliases;
$name;
}
height = 6
description = 0
key = Cufflinks genes
category = Rbm20
#
#
#[Coverage-rbm20-mutant-fwd]
#feature = coverage
#glyph = wiggle_xyplot
#database = rbm20-mutant-fwd
#height = 50
#fgcolor = black
#bgcolor = indigo
#key = Coverage Rbm 20 mutant fwd
#category = Rbm20 mRNA
#label = 0
#
#[Reads-rbm20-mutant-fwd]
#feature = match
#glyph = segments
#draw_target = 1
#show_mismatch = 1
#mismatch_color = red
#database = rbm20-mutant-fwd
#bgcolor = blue
#fgcolor = blue
#height = 5
#label density = 50
#bump = fast
#key = Reads Rbm 20 mutant fwd
#category = Rbm20 mRNA
#
#[Coverage-rbm20-wildtype-rev]
#feature = coverage
#glyph = wiggle_xyplot
#database = rbm20-wildtype-rev
#height = 50
#fgcolor = black
#bgcolor = indigo
#key = Coverage Rbm 20 wildtype rev
#category = Rbm20 mRNA
#label = 0
#
#[Reads-rbm20-wildtype-rev]
#feature = match
#glyph = segments
#draw_target = 1
#show_mismatch = 1
#mismatch_color = red
#database = rbm20-wildtype-rev
#bgcolor = blue
#fgcolor = blue
#height = 5
#label density = 50
#bump = fast
#key = Reads Rbm 20 wildtype rev
#category = Rbm20 mRNA
#[Coverage-wildtype2]
#feature = solid:wildtype2-s14
#glyph = wiggle_xyplot
#database = rbm20
#height = 50
#fgcolor = black
#bgcolor = indigo
#key = Coverage wildtype 2
#category = Rbm20 mRNA-seq
#label = 0
###############################################################################
### Annotation track configurations
# microrna genes
[mirna-genes]
feature = miRNA
database = scaffolds
glyph = generic
bgcolor = red
forwardcolor = red
reversecolor = red
key = mirbase microRNA
category = microRNA
# view deletions and snps
[shr-deletions]
feature = deletion:SHR
database = variations
glyph = generic
bgcolor = red
forwardcolor = red
reversecolor = red
key = SHR deletion
category = Variations
[shr-SNPs]
feature = SNP:SHR
database = variations
glyph = triangle
point = 1
orient = N
height = 6
bgcolor = blue
fgcolor = blue
key = SHR SNPs
category = Variations
bump density = 1
#[shr-SNPs:100000]
#database = variations
#feature = snp_density
#glyph = xyplot
#graph_type = boxes
#scale = right
[hxb-sdp]
feature = experimental_feature:hxb_sdp
database = variations
glyph = generic
bgcolor = blue
fgcolor = blue
forwardcolor = blue
reversecolor = blue
key = BXH/HXB SDPs
category = Variations
balloon click = Marker $name
Marker info from molgenis
###
### This is a query by name:
### .../api/find/org.molgenis.xgap.Marker?name=1
[GC:region]
glyph = dna
global feature = 1
database = scaffolds
height = 40
gc_window = auto
do_gc = 1
strand = both
fgcolor = red
axis_color = blue
key = GC Content
[Genes]
feature = gene:protein_coding
glyph = gene
bgcolor = dodgerblue
forwardcolor = dodgerblue
reversecolor = turquoise
label = sub { my $f = shift;
my $name = $f->display_name;
my @aliases = sort $f->attributes('Alias');
$name .= " (@aliases)" if @aliases;
$name;
}
height = 6
description = 0
key = Ensembl genes
[Translation]
glyph = translation
global feature = 1
database = scaffolds
height = 40
fgcolor = purple
strand = +1
translation = 6frame
key = 6-frame translation
[TranslationF]
glyph = translation
global feature = 1
database = scaffolds
height = 20
fgcolor = purple
strand = +1
translation = 3frame
key = 3-frame translation (forward)
[DNA/GC Content]
glyph = dna
global feature = 1
database = scaffolds
height = 40
do_gc = 1
gc_window = auto
strand = both
fgcolor = red
axis_color = blue
[TranslationR]
glyph = translation
global feature = 1
database = scaffolds
height = 20
fgcolor = blue
strand = -1
translation = 3frame
key = 3-frame translation (reverse)