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  • BLASR output - what does each column mean?

    Hi all,

    I wanted to understand the meanings of each column in the BLASR output, which looks like:

    msherri_s1_p0/20/0_269 gi|170079663|ref|NC_010473.1| 0 -1119 87.3333 4158698 4158998 4686137 6 269 269 0
    msherri_s1_p0/20/0_269 gi|170079663|ref|NC_010473.1| 1 -157 59.5855 3023879 3024050 4686137 4 169 269 0
    I understand that first column denotes the query name and second column denotes the subject genome (e.coli in this case). What about other columns? Does anyone have an idea?

  • #2
    Hi all,

    I have got the answer to this doubt. If you use -header while running BLASR, you will get the header names onto the output file. Sorry for posting the query too soon. :-)

    Comment


    • #3
      Hi all,

      I have one further question on this topic. I see the header in BLASR standard and extended output, but there are a couple of fields I don't know what they mean and I cannot find them in any documentation.

      For instance:
      qname tname score pctsimilarity qstrand qstart qend qseqlength tstrand tstart tend tseqlength mapqv ncells clusterScore probscore numSigClusters
      readX targetFileY -500 100 0 0 100 100 0 2037 2137 4950 254 2067 -17.3093 0 1

      Specially, I do not know what the ncells field means.
      Also, fields clusterScore, probscore, numSigClusters are unclear since I would need to know how they are calculated.

      Do anyone know what these mean or any place where there is more detail about these? Thank you

      Comment


      • #4
        Rather, it's the number cells used in dynamic programming, used to track performance of some of the variable-width banding methods. Nobody should be interested in this (and if I had the power of Apple, I would just remove it and let people update their parsing accordingly).

        -mark

        Originally posted by jbingham
        Not sure if you're still interested in this...

        ncells = Number of SMRT Cells

        Comment


        • #5
          These have no meaning to people, and should be removed. Sorry they are still there.

          best,
          -mark


          Originally posted by cnluzon View Post
          Hi all,

          I have one further question on this topic. I see the header in BLASR standard and extended output, but there are a couple of fields I don't know what they mean and I cannot find them in any documentation.

          For instance:
          qname tname score pctsimilarity qstrand qstart qend qseqlength tstrand tstart tend tseqlength mapqv ncells clusterScore probscore numSigClusters
          readX targetFileY -500 100 0 0 100 100 0 2037 2137 4950 254 2067 -17.3093 0 1

          Specially, I do not know what the ncells field means.
          Also, fields clusterScore, probscore, numSigClusters are unclear since I would need to know how they are calculated.

          Do anyone know what these mean or any place where there is more detail about these? Thank you

          Comment


          • #6
            Ok, I was wondering if there was anything I was missing. Thank you for your help

            Comment


            • #7
              I had a quick question about the SAM output of BLASR. What flags are needed to make a regular SAM file (specifically with a proper SAM header and the sequences in the output not just the coordinates).

              Thanks

              Edward

              Comment


              • #8
                The -sam parameter.

                Comment

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