Output gtf files

[sparthib]

Hi there,

I am using ONT reads, however, my corrected.cds.gff file has recorded the source as PacBio.
GL000194.1 PacBio exon 53590 55676 . - . transcript_id "ENST00000613230.1"; gene_id "ENSG00000277400.1";

However corrected.gtf has recorded the original source. I have two questions.

1. What's the difference between corrected.gtf and corrected.gtf.cds.gff?
2. Does having the wrong source (pacbio here) have any computational implications? Is there an argument where I can specify I am using ONT reads instead?

Thanks,
Sowmya

[pabloati]

Hi, sorry for the late reply. Regarding your questions:

1. The corrected.gtf file contains the whole annotation, while the corrected.gtf.cds.gff (now changed to corrected.cds.gff3 only has the transcripts, exons and CDS information.
2. Having the source changed to PacBio is a default action of SQANTI (which will be solved in the future). It does not affect at all any of the computations nor the results.

Thanks