The STAR alignment job finished, so I quickly ran multiqc to compare the original alignment, the first round of updated annotations, and the most recent updated gff3 file. What’s interesting is all their alignment rates look the same…

1) trimmed sequences

2) 1st round of updated gff3

3) most recent gff3 updated file

It looks like the only thing that is different is that the multiqc report from the most recent gff3 updated file has “ambiguous features”.

So does this mean that the alignment isn’t the issue?????? goddamnit.

I guess what I need to do next is try to extract the gene counts from these and compare those.