Hi all,
This post is in (cross-)reference to a question I've posted
over on Biostars. I'm asking this question here because there doesn't seem to be a separate "developer" user-group. Basically, as I understand it, the new "quantmode" allows STAR to output alignments in both genomic and transcriptomic coordinates, which is
very useful. In fact, the question I reference above is looking for a tool that's capable of projecting genomic alignments onto a set of transcriptomic coordinates (given, say, a .bam file with the genomic alignments and a gtf file with the transcript annotations). My question is, how difficult might it be to leverage the code already in STAR that maps between genomic and transcriptomic coordinates to build a tool that does this? Obviously, one could just use the existing switch when generating new alignments. However, it would also be useful to have a tool to convert genomic alignments (perhaps only readily available only as bam files) into transcriptomic coordinates. Given that my current search turned up nothing along these lines, I wonder if digging into STAR a little bit might turn up some code that is useful toward this end.
Thanks!
Rob