The next Alliance webinar is scheduled for Thursday, March 20 at noon EDT (please note: the US is on Daylight Savings Time; if your region is not, it will be a hour earlier for you). This monthâs topic is Disease annotations at the Alliance. Register by Wednesday March 19 (before midnight EDT please) to receive the Zoom link.
Interested in upcoming seminars? Theyâre posted on the Alliance Event Calendar Alliance of Genome Resources. Links to recordings of previous webinars are there too!
Sharing views in JBrowse 2 is not as easy as it is in JBrowse 1, but there is also more power in the ability to share views and data. In JBrowse 1, the entire state of the “core” view is always encoded in the URL: if you copy the URL from the browserâs location bar and send it to someone, they will get the same view as the original user. This has several limits though: if the user has loaded local data, no information about it would get into the URL. The same is true if the user has created a sequence search track: that information is not encoded in the URL.
[Read more…]JBrowse 2 provides considerable support for adding your own data. The first point about adding your own data is this: it doesnât get uploaded to anywhere. The data you add always stays where it starts, there is no âuploadingâ 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.
[Read more…]JBrowse 2 has the ability to display pairwise comparative data. At WormBase, we have comparative data between these species/assemblies:
These comparisons are made with minimap2 with the option to generate CIGAR strings. The CIGAR strings allow JBrowse to show the inserts and deletions between the compared genomes. These pre-computed comparisons can be found in a few ways from WormBaseâs JBrowse.
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