Open skagawa2 opened 2 days ago
Dear @skagawa2
Thank you for taking your time in digging into the code so deeply!
Correct if I'm wrong, but this method will separate alignments by their mapping strand reported by minimap2, right? If so, BAM file strand flag indicates whether a read sequence was reverse-complemented during mapping. It can be used if you are working with stranded protocols (i.e. dRNA), but in more frequent cDNA data reads are unstranded, and thus mapping flag is rather arbitrary since read split ~50/50.
In situation I think it will correct to use the assigned read strand, which IsoQuant computes using:
It does make algorithm more complicated, but it's certainly the right way for overlapping genes from the opposite strands. I'll if I can fix this easily.
Best Andrey
No problem! And yes you are correct, this method would separate alignments by their mapping strand. We happened to have a stranded library with trimmed polyA tails so I hadn't considered other cases and assumed you would know best haha. Please feel free to take this suggestion in any way you please, these changes just happened to work in our case.
Hello! We were looking at the exon counts again and saw some discrepancies from what we expected. This one comes from reads going on one strand counting as being excluded from the gene on the opposite strand. The example we found was with this gene below- F2RL2 and IQGAP2 (and we presume there are a handful more that get caught under this case). We saw that in
exon_counts.tsv
, the exclude counts for F2RL2 exons a sample that expressed IQGAP2 and not F2RL2 was high. This wasn't what we expected to happen when an exon is included or excluded since our reads are stranded.We came up with the following patch that we think fixes this problem, but we're not sure if this messes anything else up in unexpected ways (like the transcript classification or other parts of the pipeline). If this was also intended (that exons aren't stranded), please let us know as well!
Once again, thank you for creating this software!