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Old 04-10-2014, 10:35 AM   #1
prs321
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Default How do I calculate the coverage?

I have 4 .bam files, each one is a different treatment containing 5 replicates.

If I generate a pileup file for each one, how do I find the coverage using the pileup file?
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Old 04-10-2014, 10:52 AM   #2
GenoMax
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http://seqanswers.com/forums/showthread.php?t=1835
http://seqanswers.com/forums/showthread.php?t=42148

and several others. As you post a new thread the forum does an automatic search for previous threads on text you enter in the new post. You should be able to see those threads up at the top as you create the new thread. Search function on SeqAnswers works well too.
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Old 04-10-2014, 10:57 AM   #3
prs321
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I have, I just do not understand the technical jargon.
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Old 04-10-2014, 11:14 AM   #4
GenoMax
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Quote:
Originally Posted by prs321 View Post
I have, I just do not understand the technical jargon.
Try this then: http://bedtools.readthedocs.org/en/l.../coverage.html
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