On Apr 5, 2011 1:05 PM, "Slim Sassi" <ssa...@ccib.mgh.harvard.edu> wrote:
>
> Sean,
> 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
>

Slim,

What stats do you want to capture?  The output you gave for flagstats is
correct for single-end tophat alignments.  All reads are aligned, none are
paired, none are marked as duplicates.

Sean

> Thanks
> Slim
> 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 <ssa...@ccib.mgh.harvard.edu>
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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