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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
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.
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.
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
-x pacbio sets the following:
-k17 -W40 -r10 -A2 -B5 -O2 -E1 -L0Thank you, this is exactly what I was looking for! Is it explained in the manual? May you give me some references?
Found it!! Thank you for your time!!
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.
Is it possible to cancel a post? Can you teach me how? Thanks!
On seqanswers? No clue.