I'm curious to know if there is a standard tool or method to perform the following function:
Given some set of genomic alignments (e.g. a set of .bam files aligning to hg19), generate alignments to a set of transcripts from this genome represented by e.g. a GTF file.
So, I've seen people talk about doing the opposite before; going from alignments to the transcriptome and projecting them back to the genomic coordinates, but I want to go the other way --- a sort of "un-projection". Particularly (and this is key), alignments to a single genomic origin that correspond to multiple isoforms of a gene should generate multiple, output alignments.
Does anyone know of any software that would allow me to perform such processing?