SAM tools output question

[sowmyai]

Column 3 in SAM output format is supposed to be "the name of the reference sequence where alignment occurs" - as per documentation.
If I see an asterisk (*) in column 3, what does that indicate ? Did the read not map at all ?

[ForeignMan]

Hi,

hope you don't mind if I'll make it easy for myself and pass over to the the SAM Format Specification
(you can download it via http://samtools.sourceforge.net/SAM1.pdf )

"QNAME and FLAG are required for all alignments. If the mapping position of the query is not available, RNAME and CIGAR are set as *, and POS and MAPQ as 0. If the query is unpaired or pairing information is not available, MRNM equals *, and MPOS and ISIZE equal 0. SEQ and QUAL can both be absent, represented as a star *. If QUAL is not a star, it must be of the same length as SEQ."

Thus, you're right and the read didn't map. Hope it helps.

[sowmyai]

Thank you. But that is for QNAME and FLAG, the first and second fields. I am talking about RNAME, the third field, which is supposed to contain the name of the reference sequence that the read mapped to. It makes sense that this field should be * if the read did not map to any reference, but I just wanted to be sure.

[misko]

Hi,
Was ForeignMan referring to this part of the note?,
"If the mapping position of the query is not available, RNAME and CIGAR are set as *, and POS and MAPQ as 0."
It does mention that RNAME can be '*', when the read did not map.

Misko

[bpetersen]

I think the problem might also be different names used for your reference sequences in your reference and the sam header (or the origin of it). I've been using Bioscope and had the same problem when taking the samfile generated by Bioscope and converting it to bam with samtools. The problem for me was "chr1" in the reference and "Chr1" in the sam library file used to generate the sam header.
But that would result in * everywhere in column 3, I don't know if that's the case with your data. Well, maybe this still helps.

[sowmyai]

Thanks guys. Sorry foreignman, I missed the RNAME part of your reply.