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Old 02-27-2014, 09:59 AM   #1
naymikm
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Default Getting the part of a genome that was NOT covered by a samples reads

I have a bunch of genomes and sample reads and am looking for a way (software and method) that I can do a sequence alignment and get an output of the part(s) of the genome that were NOT covered by the sample reads. Any Ideas?
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Old 02-27-2014, 10:33 AM   #2
Bukowski
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Do the alignment and then use genomecov from bedtools:

http://bedtools.readthedocs.org/en/l...genomecov.html
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Old 02-27-2014, 11:34 AM   #3
rnaeye
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You can use bedtools too calculate genome coverage. Here is an example:
http://genescripts.com/index.php/9-n...enome-coverage
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Old 02-27-2014, 12:12 PM   #4
mchizar
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DNASTAR's SeqMan NGen will automatically create features in regions where there is no coverage as well as a coverage report that lists these regions. They also have a autoscripting tool, SeqNinja that can create new sequences from these "coverage" features.
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Old 10-28-2014, 08:36 PM   #5
naymikm
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I just realized I never thanked you all for the help! Actually, the project that I was working on here lead to my senior research project and eventually my acceptance into graduate school! I thank you all for your help!

Marcus
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