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Old 05-20-2013, 03:06 PM   #1
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Location: Chicago

Join Date: May 2013
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Default BWA-MEM and X0/X1/etc flags

Hey everyone,

I'm currently running bwa mem on some 454 single-end reads I have. My past experience with the bwa/samtools setup was with Illumina paired-end reads and using bwa aln/sampe (different projects). After looking at some of my first output for the bwa mem algorithm, I noticed there are no X0/X1 flags, which in the sampe output represent qualities such as number of best hits and number of suboptimal hits, respectively. Looking at the description of the bwa mem algorithm though on the bwa webpage (, it sounds like maybe the mem algorithm will only produce exact/unique matches, such that the X0/X1 flags are no longer needed (MEM -- maximal exact matches)? I'm interested in knowing this since I'd like to filter reads based on whether they have matches to multiple locations in the genome, and the X0/X1 tags were useful for doing this previously.

Has anyone played around with bwa mem yet and/or can comment on whether they still got X0/X1 flags when using it?


Last edited by mturchin20; 05-20-2013 at 03:18 PM.
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