Does 'samtools idxstats you_example.bam' give what you want, which sounds like reads mapped per reference sequence.
Peter On Tue, May 27, 2014 at 6:32 PM, Lana Schaffer <schaf...@scripps.edu> wrote: > Hi, > > I am aligning to fasta DB of sequences and would like to count > > The number of reads to each fasta entry by header names. > > How do I designate to bowtie to store the names in the SAM > > File and then use samtool to count them? > > > > Lana Schaffer > > The Scripps Research Institute > > Biostatistics, Informatics > > DNA Array Core Facility > > 858-784-2263 > > > ------------------------------------------------------------------------------ > The best possible search technologies are now affordable for all companies. > Download your FREE open source Enterprise Search Engine today! > Our experts will assist you in its installation for $59/mo, no commitment. > Test it for FREE on our Cloud platform anytime! > http://pubads.g.doubleclick.net/gampad/clk?id=145328191&iu=/4140/ostg.clktrk > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help > ------------------------------------------------------------------------------ The best possible search technologies are now affordable for all companies. Download your FREE open source Enterprise Search Engine today! Our experts will assist you in its installation for $59/mo, no commitment. Test it for FREE on our Cloud platform anytime! http://pubads.g.doubleclick.net/gampad/clk?id=145328191&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
