I was looking for a tool to convert a bam file in genomic coordinates to transcriptomic coordinates (using a GTF reference). Is there a fast way to do this for large bam files? Such tool would filter out reads that do not map to any transcript.
Let me know if you have any suggestions,
You'll probably get the best answer by simply mapping your reads to the transcripts directly if having transcript-based BAM files is really your goal. If, instead, you want read counts for your genomic BAM files, that can be done with several tools. If the latter is what you want, then perhaps you can clarify your question.
Hi Sean, thanks. The problem is that if I map directly to the transcripts I loose the ability to build new transcripts, find splice junctions, etc. Also in many cases I am dealing with totalRNA experiments so mapping only to transcripts I loose many reads. Let us say I already mapped all my data and just want to transform coordinates, there is no way to do this? Maybe you are right and it does not make much sense that's why it does not exist...