Hello all,
My merged bam file is about 7.4G,
"samtools flagtstat" shows that:
0 QC failure
0 duplicates
151038423 mapped (95.66%)
157886180 paired in sequencing
78943090 read1
78943090 read2
143478844 properly paired (90.87%)
148750146 with itself and mate mapped
2288277 singletons (1.45%)
3935010 with mate mapped to a different chr
1280027 with mate mapped to a different chr (mapQ>=5)
After run samtools rmdup, I got 7.2G bam file, there are reads removed.
Any explanation for this?
Does "singletons" here mean no paired read in read1 or read2 files?
Thanks
My merged bam file is about 7.4G,
"samtools flagtstat" shows that:
0 QC failure
0 duplicates
151038423 mapped (95.66%)
157886180 paired in sequencing
78943090 read1
78943090 read2
143478844 properly paired (90.87%)
148750146 with itself and mate mapped
2288277 singletons (1.45%)
3935010 with mate mapped to a different chr
1280027 with mate mapped to a different chr (mapQ>=5)
After run samtools rmdup, I got 7.2G bam file, there are reads removed.
Any explanation for this?
Does "singletons" here mean no paired read in read1 or read2 files?
Thanks
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