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  • help with sam files

    Can someone help me with this rna-seq file:

    SOLEXA1_0001:1:90:12539:8935#0 16 chr1 3003182 3 8M1708N28M * 0 0 CCCCCATACCCACCCCCCAATCCCCTACCCACCCAC BCCCCB>6@@@<CCCCCCCB>AAAA=0BCC=CCCBC NM:i:2 XS:A:- NS:i:2

    What does NS mean? I couldn't find it in sam document. Thanks.

  • #2
    NS is a tag specific to the program you're using to generate your SAM file. I can only guess what it means but it may be in the documentation of the program that generated the file.

    NM is a standard tag that's an abbreviation of Number Mismatched(or Nucleotides Mismatched). In a similar vein, NS may be Number Substituted, in which case it differs from NM by insertion/deletion of individual nucleotides.
    Because NS is not in the standard, any program that reads this SAM file can interpret it in any way. Most will simply ignore it.

    Comment


    • #3
      Thanks. The rna-seq data was processed by tophat. I think the line in my example is a junction. what do you guys think?

      Originally posted by mrawlins View Post
      NS is a tag specific to the program you're using to generate your SAM file. I can only guess what it means but it may be in the documentation of the program that generated the file.

      NM is a standard tag that's an abbreviation of Number Mismatched(or Nucleotides Mismatched). In a similar vein, NS may be Number Substituted, in which case it differs from NM by insertion/deletion of individual nucleotides.
      Because NS is not in the standard, any program that reads this SAM file can interpret it in any way. Most will simply ignore it.

      Comment


      • #4
        EDIT: has been answered
        SpliceMap: De novo detection of splice junctions from RNA-seq
        Download SpliceMap Comment here

        Comment


        • #5
          Ah, well, if it's tophat it's pretty easy to look it up in the code.
          Mismatches within min_anchor_len of a splice junction
          (from bwt_map.cpp:813 and bwt_map.h:233 in tophat source)

          It's mismatches within the anchor of a splice junction. NM covers the entire read, while NS will cover only the anchor.
          Last edited by mrawlins; 08-19-2010, 12:21 PM. Reason: Added code reference

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          • #6
            Hi, mrawlins, you are the best! Thanks!

            Originally posted by mrawlins View Post
            Ah, well, if it's tophat it's pretty easy to look it up in the code.

            (from bwt_map.cpp:813 and bwt_map.h:233 in tophat source)

            It's mismatches within the anchor of a splice junction. NM covers the entire read, while NS will cover only the anchor.

            Comment

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