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-   -   Sequence Coverage and Genome Insertion lenght from SAM (http://seqanswers.com/forums/showthread.php?t=65537)

sircamp 01-13-2016 09:59 PM

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

GenoMax 01-14-2016 03:20 AM

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.


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