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Old 01-18-2014, 06:55 AM   #1
kevindoh
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Default 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
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Old 01-18-2014, 07:20 AM   #2
rhinoceros
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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..
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Last edited by rhinoceros; 01-18-2014 at 07:23 AM.
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Old 01-18-2014, 08:04 AM   #3
lindenb
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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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