From: Heng Li <lh...@sa...> - 2012-03-27 17:00:23
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Examples? Thanks, Heng On Mar 27, 2012, at 11:10 AM, Alan Twaddle Jr wrote: > I'm trying to plot the depth of coverage but when running samtools depth > it seems to skip over bases which I presume have no alignments spanning > those regions. However, it does report some bases where there are no > alignments, though few and it nowhere near compensates for the bases that > it omits. > > After grepping through the file the number of bases for the reference > provided by samtools depth is always less then the actual number of bases. > I made sure that there would be no character incompatibilities (Ns etc.) > and still no improvement. Has anyone noticed this before? Is this a bug or > does it just not display positions with no alignments? > > I'm using samtools version 0.1.18 (r982:295) and produced bam files from > both SHRiMP and Bowtie. > > I've posted this exact message on seqanswers: > http://seqanswers.com/forums/showthread.php?t=18728 > > > -- > Alan Twaddle > Programmer/Data Analyst > GPCL Bioinformatics Analysis Core > University of Pittsburgh > 3343 Forbes Ave. > Pittsburgh, PA 15213 > (412)383-2323 > > ------------------------------------------------------------------------------ > This SF email is sponsosred by: > Try Windows Azure free for 90 days Click Here > http://p.sf.net/sfu/sfd2d-msazure > _______________________________________________ > Samtools-help mailing list > Sam...@li... > https://lists.sourceforge.net/lists/listinfo/samtools-help -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. |