JBrowse 2: Sharing views

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 browser’s 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.

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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.

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JBrowse 2: Comparative data

JBrowse 2 has the ability to display pairwise comparative data. At WormBase, we have comparative data between these species/assemblies:

  • C. elegans N2
  • C. elegans Hawaiian strain
  • C. elegans VC2010
  • C. brenneri
  • C. briggsae
  • C. inopinata
  • C. japonica
  • C. remanei 

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 WormBase’s JBrowse.

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JBrowse 2: Working with lists, bookmarks and sessions

Spreadsheet view

JBrowse 2 has a “spreadsheet view” that looks much like you might expect: a simple spreadsheet. The primary way a WormBase user might interact with the spreadsheet view is if you have a file that has a list of genomic locations that are of interest and you’d like to step through.  For example, consider this list of locations that have comments separated by a tab (so that this is a tsv file–JBrowse supports tsv, csv, VCF, BED and BEDPE files in the spreadsheet view:

  I:16,632..17,470     site 1
  I:314,852..315,768   site 2
  I:382,162..383,013   site 3--this is the good one
  I:397,470..398,755   site 4 

You can put this in the spreadsheet view by selecting “Spreadsheet view” from the Add menu:

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JBrowse 2: Searching for features and sequences

Searching in JBrowse 2 is quite similar to searching in JBrowse 1. The most common way you would look for a feature would be to type the name of a feature in the location field (that is, the field that has the current location in it, like this:

Anything that you could search for in JBrowse 1 you can search for in JBrowse 2, and there is a good reason for that: they are using exactly the same data and search indexes. So, you can look for gene and transcript names, identifiers like WBGene00006749, and allele names like pkP649.  Of course, you can also enter a location like II:100000..200000. The only difference in name searching between JBrowse 1 and 2 is that when you search for something, you will almost always get a message like this in the bottom of the screen:

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