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  • about SAM format: does QNAME contain sample information?

    I mean, how do I see if two reads come from the same sample? The manual only tells me that 2 reads having identical QNAME are paired-end, right? Could someone tell how to read QNAME, above all it's such a long string of words that must tell something other than that...

  • #2
    I just wanted to know if there's barcode for sample information (in cases of pooled sample), where would it be? Thx~~

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    • #3
      What manual?

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      • #4
        Often the QNAME is info about the instrument and the date of run, and the lane and tile and xy coordinates. The read group might tell you the sample name. That might be stored in an NM tag in the .sam file, or in the @RG header of the .sam file

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        • #5
          Originally posted by swbarnes2 View Post
          Often the QNAME is info about the instrument and the date of run, and the lane and tile and xy coordinates. The read group might tell you the sample name. That might be stored in an NM tag in the .sam file, or in the @RG header of the .sam file
          The NM tag is for the # of mismatches. Look in the RG header, if present.

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          • #6
            Originally posted by nilshomer View Post
            What manual?
            “The SAM Format Speci cation”

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            • #7
              Originally posted by nilshomer View Post
              The NM tag is for the # of mismatches. Look in the RG header, if present.
              Right, typo on my part. The SM tag might contain a sample name.

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              • #8
                Originally posted by swbarnes2 View Post
                Right, typo on my part. The SM tag might contain a sample name.
                Well, the description for the SM tag is"SM:Sample. Use pool name where a pool is being sequenced." I wasn''t putting it clearly...what I meant was, if this sample is pooled, and the origins of the sample content each is barcoded, is it possible that this infomation is contained in .SAM format? And this must be contained in the non-header sectoin...
                If it is not, how is that usually done? Is it customary that I ligate an adaptor to each sample origin, pool them, sequence, and look at the beginning of each read to see which origin of sample it came from?
                Lots of thx!!!

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