Question: Convert 2 SE bam to PE bam (alignment BWA mem)
0
gravatar for mynameliuxiang
7 weeks ago by
mynameliuxiang0 wrote:

Is there anything software which can convert two SE alignment bam files to one PE bam file?

My SE bam files are from BWA mem

bam bwa alignment • 151 views
ADD COMMENTlink modified 27 days ago by zx87547.1k • written 7 weeks ago by mynameliuxiang0
4
gravatar for Pierre Lindenbaum
7 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

Please, don't. Remap your reads.

ADD COMMENTlink modified 27 days ago by zx87547.1k • written 7 weeks ago by Pierre Lindenbaum119k

Pierre gives a good suggestion.

Merging will most likely result in incorrect values that affect things such as stranding and which read belongs to which, in later analysis. These SAM flags will become incorrect unless they will be 'fixed' on top of a merge:

  • read paired (0x1)
  • read mapped in proper pair (0x2)
  • mate unmapped (0x8)
  • read reverse strand (0x10)
  • mate reverse strand (0x20)
  • first in pair (0x40)
  • second in pair (0x80)

The same accounts for the RNEXT and PNEXT fields.

A remap will solve all these issues. Good luck!

Youri

ADD REPLYlink written 25 days ago by yhoogstrate50
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