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  • Mapping very short (<20 bp) reads

    Hi,

    I've been a SOAP2 user but recently got some very short reads (<20 bp) to map to a reference genome. Can someone please suggest an aligner which can handle the problem? SOAP seems to map only reads >30 bp.

    Thank you.

  • #2
    Originally posted by hclee View Post
    Hi,

    I've been a SOAP2 user but recently got some very short reads (<20 bp) to map to a reference genome. Can someone please suggest an aligner which can handle the problem? SOAP seems to map only reads >30 bp.

    Thank you.
    You could try bowtie or bwa

    Comment


    • #3
      Command-line BLAST could work well.

      Comment


      • #4
        I am curious about your data and brings unrelated question? Aren't <20bp reads considered ambigous? Technically its possible that good amount of your reads align to multiple regions in genome. Hence (ambiguous). Is there data to support what is a good enough read length that provides least amount of ambiguous-ness?
        I was playing around with searching and as long as I enter random sequence shorter than 20bps in general I get multiple perfect match with genome.
        Last edited by husamia; 07-15-2011, 08:51 AM.

        Comment


        • #5
          Originally posted by husamia View Post
          I am curious about your data and brings unrelated question? Aren't <20bp reads considered ambigous? Technically its possible that good amount of your reads align to multiple regions in genome. Hence (ambiguous). Is there data to support what is a good enough read length that provides least amount of ambiguous-ness?
          I was playing around with searching and as long as I enter random sequence shorter than 20bps in general I get multiple perfect match with genome.
          I was wondering about this too. Shorter than 20 you cannot differentiate them from random sequences.

          Comment

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