multiple alignments with BWA

efoss · 08-07-2011, 12:37 PM

The manuscript "Fast and accurate short read alignment with Burrows–Wheeler transform" says this:

"It [BWA] performs gapped alignment for single- end reads, supports paired-end mapping, generates mapping quality and gives multiple hits if required."

I would like to use identify all reasonable alignments for my reads, since if I see a read aligning to many places in the genome, I know to be skeptical of that alignment. However, I don't see this option in BWA. Can anyone help me out here?

Thanks.

Eric

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
BWA and sub-optimal alignments	LauraR	Bioinformatics	0	02-10-2012 08:46 AM
How many multiple alignments to allow?	hlwright	Bioinformatics	0	04-14-2011 12:40 AM
BWA: suboptimal alignments	ElMichael	Bioinformatics	2	03-29-2011 02:31 PM
merging bwa alignments	arnkas	Genomic Resequencing	5	07-07-2010 08:26 AM
BWA alignments and time	cggj	Bioinformatics	5	05-13-2010 11:41 AM

08-07-2011, 12:37 PM	#1
efoss Member Location: Seattle Join Date: Jul 2011 Posts: 98	multiple alignments with BWA The manuscript "Fast and accurate short read alignment with Burrows–Wheeler transform" says this: "It [BWA] performs gapped alignment for single- end reads, supports paired-end mapping, generates mapping quality and gives multiple hits if required." I would like to use identify all reasonable alignments for my reads, since if I see a read aligning to many places in the genome, I know to be skeptical of that alignment. However, I don't see this option in BWA. Can anyone help me out here? Thanks. Eric