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  • Cut Sites Per Megabase

    Hey guys,

    I can't seem to find the right tool to do this. I was wondering if anyone had advice on how to approach.

    I am attempting to get the number of cut sites per megabase for the whole genome (given a recognition site). I'd rather not write all the code from the bottom up. Does anyone have a tool that would do this efficiently? Or a strategy for coding it myself that doesn't involve days of work?

    Thanks in advance

    K

  • #2
    If it's a fasta file,

    Code:
    grep -v ">" yourFile.fasta | grep -c "ATGCCCGC"
    Just replace the seq with whatever..

    edit. This tells the total number. You'd obviously have to divide with seq length to get per whatever..
    Last edited by rhinoceros; 01-18-2014, 08:23 AM.
    savetherhino.org

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    • #3
      use Biostar86480 https://github.com/lindenb/jvarkit/wiki/Biostar86480 and pipe the output in bedtools/groupby http://bedtools.readthedocs.org/en/l...s/groupby.html

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