On 27 May 2014, at 10:58, Wolfgang Maier
<wolfgang.ma...@biologie.uni-freiburg.de> wrote:
> On 22.05.2014 20:59, Kate Im wrote:
>> 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.
In particular (see ยง2, 4.1 of that document), there is the common convention
for pairs in which just one end is mapped, of giving both reads the RNAME and
POS (3rd and 4th) columns of the mapped end. This has the useful side-effect
of bringing the unmapped end alongside its mate when the file is
coordinate-sorted.
John
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