I only have one bam file. There is no place to store other reads.
2016-12-15 8:53 GMT-05:00 Thomas W. Blackwell <tbla...@umich.edu>:
>
> 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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