IsoAnnotLite protein features are not transferred

[mintstella0419]

Dear SQANTI3 team,

I have run IsoAnnotLite using my SQANTI output hoping to map the protein domains on my gff3 file, but none of the features with PosType=P are transferred. Is this a known issue or is there any reason why it might have happened?

Thanks!

[aarzalluz]

Hi @mintstella0419,

This could happen due to a couple of reasons:

• All the isoforms in your input transcriptome were predicted as non-coding (perhaps if you run SQANTI3 QC with the --skipORF flag).
• No overlaps, total or partial, were found between the CDS of the transcripts in the GFF3 file and the transcripts in your input GTF file.

However, I would need some more details in order to spot the problem:

• Which organism and GFF3 file are you working with?
• Which reference genome/transcriptome did you use to generate your input GTF file?
• What was your SQANTI3 input command?
• Are the rest of the SQANTI3 output files generated correctly?
• Are transcript-level features transferred, but not protein fetaures?

Best,

Ángeles

[carolinamonzo]

Closing since the user did not give any more information. We agree with the ideas of why this happened that Ángeles suggested.