On 01.06.2014 22:15, carol white wrote: > > Another question is POS is the 1-based leftmost POSition in the case of > both reverse and forward strand or is the 1-based RIGHT most POSition in > case of reverse strand? > > Look forward to your reply, > >
An aligned read sequence is always reported in the orientation of the reference. So if you have a read aligned to the reverse complement of the reference, its sequence is reported as the reverse complement of its original sequence (like in a fastq file) and then the reverse complement flag bit is set to indicate this fact. In other words, if you have a read that has the reverse complement flag bit set, you need to reverse complement its sequence to get its original sequence. The value of the POS field is always the 1-based leftmost position of the stored read sequence on the reference, so, in this case, it is the position of the original read's 3' end on the reference. Hope that's understandable, Wolfgang ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
