displaying gff3 files - sorted vs. unsorted

[aldrin]

Hi IGV team.

We have 2 gff3 files.  They are essentially the same in terms of contents, except that one is sorted by chromosome number and by annotation type (exon, cds, UTRs, etc...) while the other one is unsorted.

When we loaded and displayed them both on IGV 2.1.24, the unsorted gff3 displayed well but the sorted gff3 did not.

Is this expected?  Can someone from IGV team please help us understand what is going on and maybe fix it as well, if possible? 

Note:  I tried attaching copy of each gff3 file but I got this error (

An error (#340) occurred while communicating with the server

) when I clicked POST.  May be files are too big for posting.  So if needed, please let me know where to send the files.

Thank you.

-Aldrin

[Jacob Silterra]

If the gff file is indexed it must be sorted by chromosome (it doesn't matter what order the chromosomes are in as long as they are together) and start position. Sorting by annotation should have no effect

Can you be more specific about what you mean by "displayed well"? Screenshots would be helpful.

You can upload the files to ftp.broadinstitute.org/incoming. This is a read-only ftp site, please let us know the file names when you've done so.

-Aldrin

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Jacob Silterra
Software Engineer
Broad Institute

[Jacob Silterra]

The issue with these files is actually that the "sorted" version has some fields which are separated by spaces, rather than tabs. The GFF spec requires fields to be separated by tabs. Our current implementation was just skipping those lines, in a future release an error may be thrown.

-Jacob