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  • discarding homopolymer reads

    I'm looking for a script that I could use to remove all homopolymer reads from my 100 bp PE reads. These are unusually overabundant in my sample.

    I can't seem to find a script that will do this. I've tried to use fastx_clipper, but defining the adapter as a homopolymer, and that didn't work (defined adaptor too long?).

    Any ideas?

  • #2
    Originally posted by gevielr View Post
    I'm looking for a script that I could use to remove all homopolymer reads from my 100 bp PE reads. These are unusually overabundant in my sample.

    I can't seem to find a script that will do this. I've tried to use fastx_clipper, but defining the adapter as a homopolymer, and that didn't work (defined adaptor too long?).

    Any ideas?
    I wrote a script in python3 that does that. You may find that useful. If you're interested, email me [email protected]

    Comment


    • #3
      Great, thanks!! I'll shoot you an email.

      Comment


      • #4
        You could also use dust via prinseq. You might have to play around with the scoring to get a sense of the type of reads you're losing, but it should become pretty clear when you're dumping only very low complexity stuff, like say trinucleotide repeats and shorter.

        Comment


        • #5
          Dust

          I am using DUST to perform this task.
          But DUST do not remove the reads with low complexity. It put the low complexity bases in lowercase.
          I don't know how to remove those lowercase reads after running DUST.

          How do you guys do to remove those reads after running DUST?

          Comment

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