JBrowse 2: Adding your own data

JBrowse 2 provides considerable support for adding your own data. The first point about adding your own data is this: it doesn’t get uploaded to anywhere. The data you add always stays where it starts, there is no “uploading” of the data. This is an important point if you are worried about the privacy of your data. JBrowse supports several common formats for genomics data, including GFF, VCF, BED, BigWig, BigBed, and BAM/CRAM. For a complete list of supported formats, see the JBrowse 2 documentation. For supported formats, the only caveat is that the reference sequence names should be names that the WormBase JBrowse will recognize. In this case, that means chromosome names like I, II, etc for C. elegans should be used, though JBrowse also understands aliases like chrI and chrII, which is what the UCSC Genome Browser uses. As a first example of what can be done with your own data, we created a GFF file that has entries for polymorphisms that are found in the Hawaiian strain of C. elegans. We did this with a simple `grep` command, like   grep “\tVariation_project_Polymorphism\t” c_elegans.PRJNA13758.WS289.annotations.gff3.gz | grep CB4856 > hawaiian_variants.gff To create a track for this data in the N2 JBrowse instance, there are two places I can find the “Add track” option. Both of these reside in the track selector, so if it’s not already open, click the big “open track selector” button in the linear genome view that appears when there ar...
Source: WormBase - Category: Genetics & Stem Cells Authors: Tags: tutorials jbrowse2 Source Type: news