Closed Akazhiel closed 2 years ago
Can you clarify where exactly (which output of gffcompare?) has that "number of samples reported" that greatly exceeds the max number of samples you have?
It’s the gffcmp.combined.gtf. It has a field called “num_samples”, which is reporting more samples than I am working with.
This only happens when duplicate/redundant (matching) transfrags exist in a sample GTF.
Unfortunately even StringTie seems to produce such structurally redundant transfrags sometimes -- those can happen for isoforms with the same intron chain (or single-exon transfrags) but with different TSS/TES as suggested by read coverage.
I've come across what could possibly be a bug. When running gffcompare to merge multiple GTF files using a reference file, the number of samples reported sometimes greatly exceeds the max number of samples I'm working with which is 60, and when I take a look at the tracking file, as it's to be expected, the sample number is within the expected range. There may be a problem on how gffcompare counts the
q
occurrences and reports it.