TracNav(xQTL)?

xQTL workbench - Import new data

Geno- and phenotypic data

• A special importer for this kind of data is available under the tab Import data.
• First, choose the Investigation where you want to upload into.
• Select a geno, pheno or map file in the corresponding location and press Upload.
• Repeat this process to upload more data.

Please note:

• The filename is used as data matrix name. Choose it carefully.
• The created data matrices are tagged as Rqtl analysis pheno or geno datasets. They will appear when running a default QTL analysis.
• When uploading a map file, marker and chromosome annotations are created in the database.
• Individual and trait (phenotype) annotations are not automatically created.
• It is good practice to also annotate your individuals and traits. In fact, for certain analysis types this is required. (Genetical Genomics, trait heritability estimation, etc)
• Different seperators are recognized in all file uploads. Usual ones include tab, whitespace or comma.

Help: my QTL analysis fails!

Please check the following:

• The markers in the genotype matrix must be annotated in the map file. The names must exactly match. Check use the Inspector tool in View data to verify data consistency. You can always manually add or manipulate markers at any point using View annotations, click Markers.
• For a correct new data set, the exact same individual names must be used in the genotype and phenotype file.
• The QTL analysis needs to know which type of cross was used. It looks at the annotation of the first individual of the genotypes to get cross type from the ontologyReference field. Set this to e.g. xgap_rqtl_straintype_riself to indicate the cross is a recombinant inbred line by selfing. The coding is taken from Rqtl.

Help: my individuals are not on the first line!

The importers for genotype and phenotype files expect you to put individuals on the first line, making them the column headers. If your rows and columns are 'flipped' and would need transposing, don't worry. Just upload the files. You should just re-annotate your rows and columns by going to Browse data in the main menu, then select View data and find your recent uploaded data matrix. Click Show additional fields to show the full annotation. Use the dropdown menus to swap the values of FeatureType (columns) and TargetType (rows). Press save the changes.

Other data

Annotations:

• Annotation data should be added using the Add new record button in the corresponding subtab of View annotations of your choosing.
• Alternatively, you can perform a CSV file batch upload in the menu File, or upload data via the R api.

Data matrices:

• Matrix data can be added by creating a new Data record in the View data tab.
• The Manager viewer will inform you there is no data linked to this entry, and you can upload it via direct CSV input or file.