On 22.05.2014 20:59, Kate Im wrote: > I am using samtools flagstat to get some basic statistics on my > alignment and I noticed that the number of unmapped read (estimated by > subtracting the reported number of mapped reads from the reported number > of total reads) is always higher than the number of sequences with an " > * " in the third column of the SAM file. Shouldn't these be the same? >
Ideally, yes, but the SAM/BAM format specifications (http://samtools.github.io/hts-specs/SAMv1.pdf) say that: "Bit 0x4 [in the FLAG field] is the only reliable place to tell whether the segment is unmapped. If 0x4 is set, no assumptions can be made about RNAME, ..." so it is up to your aligner how to format unmapped reads except for the FLAG bit. Best, Wolfgang ------------------------------------------------------------------------------ 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
