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  • Bowtie colorspace output has less NT than input reads

    Hi,

    I am using bowtie for colorspace alignment. My data are 35nt reads (36nt if the first T is included). In the bowtie default output file, the decoded sequence space reads has only 33 NT displayed.

    my command is:

    bowtie -t -q -p 7 -C -n 3 -a --best MyGenomeSeq MyInput.fastq > MyOutput.aln &

    Could anyone explain this?

    Thanks,
    Song Li

  • #2
    Hi SongLi,
    one of the options in bowtie is trimimng bases from:
    " -5/--trim5 <int>
    Trim <int> bases from high-quality (left) end of each read before alignment (default: 0).

    -3/--trim3 <int>
    Trim <int> bases from low-quality (right) end of each read before alignment (default: 0). "

    maybe you used it?

    Ilia

    Comment


    • #3
      Hi,

      Thank you for the reply. My command is included in my previous post. I did not use --trim unless it was default for colorspace alignment.

      Best,
      Song

      Originally posted by zhidkov.ilia View Post
      Hi SongLi,
      one of the options in bowtie is trimimng bases from:
      " -5/--trim5 <int>
      Trim <int> bases from high-quality (left) end of each read before alignment (default: 0).

      -3/--trim3 <int>
      Trim <int> bases from low-quality (right) end of each read before alignment (default: 0). "

      maybe you used it?

      Ilia

      Comment


      • #4
        --trim option suppose to be 0 by default...

        Comment


        • #5
          Ok, found this:


          think it has the answer you looked for

          PS
          Learned something new myself, thank you

          Comment


          • #6
            Thank you for pointing out this link.



            Originally posted by zhidkov.ilia View Post
            Ok, found this:


            think it has the answer you looked for

            PS
            Learned something new myself, thank you

            Comment

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