I’m trying to use DESeq2 to analyze differential expression between Salmon quant files with a .gff3 file as my gene mapping format, but I’m getting a generic error that suggests I carefully check my inputs and contact an administrator.
I’ve seen some other issues similar to this using a gene-to-transcript mapping file, but that hasn’t helped resolve my issue trying to use a .gff3 file.
My trimmed reads were input to salmon using ensembl cDNA .fa files as the transcript index with sequence-specific and GC bias corrections, but did not include a gene-to-transcript mapping file as I figured I could accomplish this in DESeq2 with the .gff3. I’m wondering if this is my problem? I’m also wondering if there’s a way to find a gene-to-transcript mapping file for a species of interest, I’m struggling to come up with a way to generate one conveniently.