Likely a mixup in file names. Use the bam header information
to figure out what data are actually in each file. Perhaps
there are '@RG' or '@PG' lines in the headers that will tell
you what data are in each file.
- tom blackwell -
On Wed, 14 Dec 2016, Michael Peng wrote:
> Hi,
>
> I run
>
> samtools view -bh old.bam > new.bam
>
> the new.bam is 98G while the old.bam is 110G.
>
> But the flatstat for old.bam is
> 713835589 + 0 in total (QC-passed reads + QC-failed reads)
> 5098877 + 0 secondary
> 0 + 0 supplementary
> 45662312 + 0 duplicates
> 706481423 + 0 mapped (98.97% : N/A)
> 708736712 + 0 paired in sequencing
> 354368356 + 0 read1
> 354368356 + 0 read2
> 682853462 + 0 properly paired (96.35% : N/A)
> 696021484 + 0 with itself and mate mapped
> 5361062 + 0 singletons (0.76% : N/A)
> 9163046 + 0 with mate mapped to a different chr
> 4873946 + 0 with mate mapped to a different chr (mapQ>=5)
>
>
> The flagstat fo new.bam is
> 736285019 + 0 in total (QC-passed reads + QC-failed reads)
> 5388533 + 0 secondary
> 0 + 0 supplementary
> 30551497 + 0 duplicates
> 730966740 + 0 mapped (99.28% : N/A)
> 730896486 + 0 paired in sequencing
> 365448243 + 0 read1
> 365448243 + 0 read2
> 709064844 + 0 properly paired (97.01% : N/A)
> 722413152 + 0 with itself and mate mapped
> 3165055 + 0 singletons (0.43% : N/A)
> 9176396 + 0 with mate mapped to a different chr
> 4811953 + 0 with mate mapped to a different chr (mapQ>=5)
>
>
> There are more reads in new.bam with smaller file size. A little confused
> what happen here.
>
>
> Best,
> Gang
>
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