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papori

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Join Date: Dec 2010

Posts: 181
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scale to RPM for genomecov - bedtools

05-04-2014, 03:05 AM

Hi,
i am not sure how to use the "scale" function in bedtools genomecov.
i want to normalize the output by Reads Per Milion.
i used this:
bedtools genomecov -ibam file.bam -d -scale 1000000

is it right?

Thanks,
Pap
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