Extract Simple Alignment From Sam/Bam

Question

[Revh]

Hi

I have annotated a number of RNA reads with the originating gene, and keep them in a bam file.

Now I want to extract a simple alignment for each gene from this sam file. I don't care about genomic location, quality of read or any other data. Only the aligned sequences corresponding to that gene. One alignment file (something like .aln) for each gene.

Any ideas on how to do that?

[Pierre Lindenbaum]

what about using an alignment viewer like IGV ?

Answer 1

[Jeremy Leipzig]

I would actually suggest collecting the the reads and re-aligning against that gene using a Smith-Waterman implementation.

The Bio* packages have mature tools to display pairwise alignments - CIGAR is too goofy a format for this task.

[Revh]

Thanks, I ended up doing just that.