Question: Extract Simple Alignment From Sam/Bam
gravatar for Revh
8.2 years ago by
Revh60 wrote:


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?

alignment sam • 2.8k views
ADD COMMENTlink modified 20 months ago by Biostar ♦♦ 20 • written 8.2 years ago by Revh60

what about using an alignment viewer like IGV ?

ADD REPLYlink written 8.2 years ago by Pierre Lindenbaum127k
gravatar for Jeremy Leipzig
8.2 years ago by
Philadelphia, PA
Jeremy Leipzig19k wrote:

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.

ADD COMMENTlink written 8.2 years ago by Jeremy Leipzig19k

Thanks, I ended up doing just that.

ADD REPLYlink written 8.2 years ago by Revh60
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