Question: bwa: RNAME of chimeric reads in sam file
gravatar for VHahaut
3.6 years ago by
VHahaut1.1k wrote:


I am currently aligning some sequences that contain numerous chimeric reads using bwa (paired-ends). Usually, first third of the R1 is on Chr1 and the rest on Chr18, the R2 is fully mapped to Chr18.

I was wondering how bwa was aligning those reads. If we look at the sam file produced after alignment, what will be the RNAME of the read R1 (chr1 or chr18)? And how is it decided?

Thanks in advance!

bwa • 1.4k views
ADD COMMENTlink modified 3.6 years ago by Pierre Lindenbaum127k • written 3.6 years ago by VHahaut1.1k
gravatar for Pierre Lindenbaum
3.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

BWA should create multiple SAM records for the same Read. A first SAM record will be mapped on chr1 and will contains a 'SA:X' attribute containing the alternate alignments, the cigar string will be soft-clipped. The other reads will be the instances of the 'SA:X' tag above = the other alignements, and they will be flagged as 'supplementary alignement'.

ADD COMMENTlink written 3.6 years ago by Pierre Lindenbaum127k

Thanks! Indeed after looking for the duplicated read names I found them.

ADD REPLYlink written 3.6 years ago by VHahaut1.1k
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