You are correct,  I did use tophat. Can you or anyone suggest a program for 
BAM/SAM stats where the alignment was done with tophat

On Apr 5, 2011, at 12:51 PM, Sean Davis wrote:

> Hi, Slim.
> My guess is that you used an aligner that outputs only aligned reads
> (tophat, for example) and that the input was single-ended.  If that is
> the case, then what you see below is exactly as expected.  If not,
> then you might need to be more specific about how you generated the
> BAM file.
> Sean
> On Tue, Apr 5, 2011 at 12:31 PM, Slim Sassi <> 
> wrote:
>> Hello,
>> I tried to use NGS: SAM Tools ->flagstat on a BAM files for basic stats, but
>> I got results like you see below. It doesn't seem to be working. Any
>> suggestions?
>> 26584869 in total
>> 0 QC failure
>> 0 duplicates
>> 26584869 mapped (100.00%)
>> 0 paired in sequencing
>> 0 read1
>> 0 read2
>> 0 properly paired (-nan%)
>> 0 with itself and mate mapped
>> 0 singletons (-nan%)
>> 0 with mate mapped to a different chr
>> 0 with mate mapped to a different chr (mapQ>=5)
>> Thanks
>> Slim
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