**Error SEQ2: Some exons have differing strands

[lisagrigoreva]

Hi,

I'm trying to process Arabidopsis data using your tool. However, there is an error that arises I'm providing gff and full genome fasta file

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**Error SEQ2: Some exons have differing strands
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Should I remove these exons?

[lisagrigoreva]

Solved. You need to subset only genomic sequences from gtf and fasta (probably this is a problem with annotation)

[gwct]

Great! Glad it seems to be working now. We did code that all exons within a transcript should be on the same strand in the annotation file, and I think this is expected for most annotation pipelines. But GFT/F files are notoriously un-standardized, so we're always on the look out for these discrepancies.

[milesroberts-123]

I've ran into this same problem with annotations for a few different plant species. Would it be possible to turn this error into a warning where degenotate automatically drops the problematic transcript(s) before continuing with the analysis?

Of course, just manually removing the problematic transcripts from the GFF file is a pretty easy fix too

[gwct]

Will work on converting these to warnings and update when I push the code.

[gwct]

I've changed theses from errors to warnings and pushed the code https://github.com/harvardinformatics/degenotate/pull/34, so if you've downloaded from github you can update via a git pull or by downloading v1.1.3 . It should be up on bioconda soon as well.

[milesroberts-123]

Very cool! Thank you so much!

[gwct]

Updated version now up on bioconda.