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Old 04-04-2013, 02:21 AM   #1
Location: barcelona

Join Date: Mar 2013
Posts: 18
Question genome coverage


Which one do you think is the best and easier alternative to Picard Statistics to measure basic genomic metrics, such as virus genome coverage?

I am working on Mac OSX's Terminal and Linux.

marco12345 is offline   Reply With Quote
Old 04-04-2013, 09:00 PM   #2
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Location: Sydney, Australia

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If you like working in R, then you can use the package Rsamtools to read in the mapping file and GenomicRanges to get coverage for every base, then divide by the size of the genome to calculate how many times you covered the genome.
Dario1984 is offline   Reply With Quote

coverage, genome, gwas, mac osx, virus

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