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GMOD / Apollo

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.
http://genomearchitect.readthedocs.io/
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Indels in long RNAseq reads interpreted as introns when used to make annotations. #2085

Closed fayerodgers closed 5 years ago

fayerodgers commented 5 years ago

When making a gene model from a full length RNASeq read, indels seem to be being interpreted as introns. Eg, when making annotations from the top two reads here:

screen shot 2019-03-01 at 10 16 25

This is on the master branch from 19th Feb (2.3.1-snapshot).

Thanks!

nathandunn commented 5 years ago

@fayerodgers I may have fixed this already (unsure). Could you retry against master (should be 2.4.0-snapshot)?

If not, would it be possible to provide BAM data and/or a JBrowse directory at least with the relevant read track and sequences to speed up the fix?

Thanks,

fayerodgers commented 5 years ago

Cheers, will retry with master and let you know!

fayerodgers commented 5 years ago

So it looks like with the current master I can't make any genes from RNAseq reads at all (though making pseudogenes and ncRNAs from them seems to work). I've copied an example jbrowse directory here for you: ftp://ftp.ebi.ac.uk/pub/databases/wormbase/STAFF/fr7/t_muris_jbrowse/ (both of the BAMs in the BAM directory should illustrate the problem). Cheers

nathandunn commented 5 years ago

@fayerodgers Okay. I will take a look.

nathandunn commented 5 years ago
nathandunn commented 5 years ago

The problem is that https://github.com/GMOD/Apollo/blob/master/client/apollo/js/JSONUtils.js#L276 fails because the test_feature has no type.

https://github.com/GMOD/Apollo/blob/master/client/apollo/js/JSONUtils.js#L215 needs to be called from DraggableHTMLFeatures

nathandunn commented 5 years ago

@fayerodgers

You should be able to use master to add genes now.

Can you give me the location and what you expect to see (if it is not working the way you want still).

We changed some things to fix this behavior in #1788. As such, we created an exon for each match when you drag it up (as opposed to a single large exon).

nathandunn commented 5 years ago

Sorry @fayerodgers I’m being dense. I’ll see if I can’t come up with a fix that preserves the exon over the indels.

nathandunn commented 5 years ago

@fayerodgers this should be working on master now. Let me know if you run into any problems with it (or expect different behavior).

fayerodgers commented 5 years ago

That's fixed it, thanks very much for the speedy response!