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Old 01-13-2016, 09:59 PM   #1
sircamp
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Location: Italy

Join Date: Jan 2016
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Default Sequence Coverage and Genome Insertion lenght from SAM

Hi to everyone,

I'm quite new of this science, and I'm looking for solve a problem.

I've a SAM file generated by BWA and must to calculate two different things:

1) Genome insertion lenght ( for plotting mean and standard dev )
2) Sequence Coverage


I've calculate the insertion lenght with this operation abs(col[3]-col[7]) made for each row.

The main problem is that i can understand how to calculate sequence coverage from SAM file, i must implement the algorithm in python or perl, but the prolem is not "the language" is wath operation i need to do?

Anyone have some ideas?

thanks in advance to everyone
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Old 01-14-2016, 03:20 AM   #2
GenoMax
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genomecov (http://bedtools.readthedocs.org/en/l...genomecov.html) or coveragebed (http://bedtools.readthedocs.org/en/l.../coverage.html) tools from Bedtools package can do this operation. You can find graphical representation of what needs to be done (since you want to write your own code) at those links.

Last edited by GenoMax; 01-14-2016 at 03:22 AM.
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