User: mynameliuxiang

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Posts by mynameliuxiang

<prev • 5 results • page 1 of 1 • next >
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Convert 2 SE bam to PE bam (alignment BWA mem)
... 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 ...
alignment bwa bam written 6 months ago by mynameliuxiang0 • updated 5 months ago by zx87548.2k
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Comment: C: samtools filter proper paired alignment
... thank you, i got it. I mistook about supplement alignment and second alignment. your post is very useful. ...
written 7 months ago by mynameliuxiang0
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Comment: A: samtools filter proper paired alignment
... However It is stilled confused that "proper paired (filtered by flag -f 2)" bam file have different count of read1 and read2 ? ...
written 7 months ago by mynameliuxiang0
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Comment: C: samtools filter proper paired alignment
... Yes, I got this bam by BWA mem. I want to get propered alignment, using fixmate to filter, is that right? samtools fixmate test1.uniq.prop.pair.bam a.bam 33117 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 33117 + 0 mapped ...
written 7 months ago by mynameliuxiang0 • updated 7 months ago by h.mon27k
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samtools filter proper paired alignment
... I want get proper paired alignment here is my scripts $ samtools view test1.v2.4.reordered.bam -f 2 -bS - 1> test1.uniq.prop.pair.bam Next using flagstat check result bam samtools flagstat test1.uniq.prop.pair.bam 33117 + 0 in total (QC-passed reads + QC-failed reads) 0 + ...
alignment written 7 months ago by mynameliuxiang0

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