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GMOD / jbrowse

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
http://jbrowse.org
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Support GFF3 Gap attribute #963

Open nathanweeks opened 6 years ago

nathanweeks commented 6 years ago

It would be convenient if JBrowse could render spliced alignments from tabix-indexed GFF3 files using the CIGAR string in the GFF3 Gap attribute (e.g., produced from gmap's gff3_match_est format), rather than requiring a less-storage-efficient approach of having a separate GFF3 line for each aligned segment.

cmdcolin commented 6 years ago

You might also consider BigBed format which keeps all info on the same line. The gtf2bed script https://github.com/dasmoth/gtf2bed and this PR can go some ways towards accomplishing this https://github.com/GMOD/jbrowse/pull/944

nathanweeks commented 6 years ago

Hi @cmdcolin, thanks for the heads up regarding the forthcoming BigBed support in JBrowse. BED files appear to lack support for arbitrary key/value pairs like the GFF3 9th column, and our use case is to display interspecific gene model primary transcript alignments with their functional annotation.

Until GFF3 Gap attribute support is available in JBrowse, it seems like modifying our processing pipelines to handle SAM / output BAM might be the most realistic alternative.

cmdcolin commented 6 years ago

It's not necessarily true that BED file doesn't allow arbitrary key value pairs. The bed file "autosql" concept allows arbitrary information encoding, and this can be converted from other formats using the gtf2bed program mentioned before

See https://github.com/dasmoth/gtf2bed/blob/master/gencode.as as an example

cmdcolin commented 6 years ago

If it is easier to support GFF3 Gap, I am all for that too. I just thought I'd point out the possible alternative :)

nathanweeks commented 6 years ago

Thanks for the pointer regarding AutoSQL support in BigBed; I had missed that. Will https://github.com/GMOD/jbrowse/pull/944 add support for that as well?

cmdcolin commented 6 years ago

@nathanweeks now there is some basic autosql support :)

nathanweeks commented 6 years ago

@cmdcolin : cool, looking forward to trying it out!

nathanhaigh commented 6 years ago

Just to add a resource link which may be useful: