I have a large .BAM file containing cleaned reads of RNA Seq data from a partnered sequencing project. My goal is to take existing protein sequences and align them to the RNA Seq data in order to identify corresponding sequence regions. I have looked into using multiple resources to do this (BLAST command line, genome workbench, picard), but have not found much success as my bioinformatics experience only goes so far as R, muscle, and the online BLAST tool. I was wondering if anyone had any recommendations or experience with something like this that they could offer.
Thank you in advance.