Closed MengjunWu closed 3 months ago
Assigning to @jmattick
Hi @MengjunWu,
collapse
filters based on the following:
rc
tag. These minimum values can be changed using the following options.
Alignment Filter Options:
--min-aln-coverage FLOAT Ignore alignments with less than minimum query read coverage. [0.99]
--min-aln-identity FLOAT Ignore alignments with less than minimum alignment identity. [0.95]
Hi, I have some problems with isoseq collapse. While most of my reads (90%) are mapped, almost half of them are filtered out after isoseq collpase. I was wondering how do you calculate coverage and identify? I am using the mg tag to get the identity, and calculating coverage per read as number of matches and mismatches in the cigar string divided by the read length, but I get much less reads filtered out than by isoseq collapse with the same thresholds. Are either coverage or identity calculated differently?
Many thanks Mengjun