Sean,

I only wanted to start collecting stats with flagstats but knew that I needed 
something else to get everthing needed. 
I would like to know:
% that didn't pass QC
% mapped
% reads in exons/introns/intergenic regions

and then, knowing that this is more complicated, I wanted to measure bias 
within transcripts (for example 3' versus 5'). Of course I am assuming that 
there is a consistent bias.


Thanks
Slim



On Apr 5, 2011, at 1:50 PM, Sean Davis wrote:

> 
> 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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> > >> it is
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> >

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