FileNotFoundError: missing refAnnotation_***.genePred file? about sqanti2

[Magdoll]

Hi @rebailey ,

This error is indicating it has trouble converting your reference GTF Brassica_napus.annotation_v5.gtf into .genePred format, for one reason or another.

Try running from command line:

gtfToGenePred \
    -genePredExt -allErrors -ignoreGroupsWithoutExons \
     Brassica_napus.annotation_v5.gtf\
     test.genePred

This is pretty much the command that SQANTI2 runs to convert the annotation GTF to genePred format.
-Liz

[rebailey]

Hi @Magdoll,

Thanks for your response. After running the command you provided I still get a similar error:

Brassica_napus.annotation_v5.gtf doesn't appear to be a GTF file (GFF not supported by this program)

The GTF annotation file I'm using (a few lines posted above for reference) came from a GFF to GTF conversion using gffread. To my eye it seems to be in the correct format that SQANTI2 is expecting. Any tips to get around this, or is it possible the conversion didn't actually work properly?

Thanks again!

• Ryan

[rebailey]

Update:

I was able to run gtfToGenePred successfully using a new GTF file which I converted from an updated GFF3 annotation (a sorted/fixed version of the original, made by a colleague).

Running sqanti_qc2.py now and will update.

Thanks again for the assistance!

Cheers,
Ryan