BWA_MEM on PacBio Reads
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9.6 years ago
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Hello, can anybody explain me please how does the BWA-mem -x pacbio (Release 0.7.10, default settings) algorithm work?

I found this interesting blog but it is still not clear to me.

Can you also suggest me how to unambiguously distinguish mapped/unmapped and multimapping reads?

Thank you very much!!

Aurora

PacBio BWA-mem • 4.3k views
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Hello auroramaurizio1!

It appears that your post has been cross-posted to another site: SEQanswers.

This is typically not recommended as it runs the risk of annoying people in both communities.

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So do you want to know how the algorithm works (read the paper) or how to distinguish between mapped/unmapped and multimapping alignments? The latter can be done with samtools.

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Thank you Devon Ryan for the reply, i'll delete the one in SeqAnswers :). Do you work with these tools? I would greatly appreciate it if you kindly give me some feedback! I wanted to know how the -x pacbio option works ... originally BWA-mem was not designed with Pac-Bio in mind. I wanted also to now specifically which tags to use to discriminate between mapped/unmapped and multimapping alignments. Thank you so much, A

2014-09-08 12:08 GMT+02:00 Devon Ryan on Biostar

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-x pacbio sets the following: -k17 -W40 -r10 -A2 -B5 -O2 -E1 -L0

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Thank you, this is exactly what I was looking for! Is it explained in the manual? May you give me some references?

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Found it!! Thank you for your time!!

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For mapped unmapped, use samtools and filter according to the flag field (read the SAM spec). For multimappers, I think bwa sets one of the auxiliary tags to "R", but regardless it makes more sense to filter by MAPQ.

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Is it possible to cancel a post? Can you teach me how? Thanks!

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On seqanswers? No clue.

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