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Hello,
How can I calculated my coverage for amplicons?
Thank you very much in advance
How can I calculated my coverage for amplicons?
Thank you very much in advance
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Do you have a bam and bed? Coverage per amplicon or average coverage in bam?Last edited by cmccabe; 10-29-2015, 03:01 PM. -
Thank you very much for your response. Yes, I have bam and bed file. I would like calculate the coverage per amplicon. What it is the average coverage in bam? Is it important?
Thank you in advanceComment
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The average coverage of a bam file is all captured bases outputed as one #, such as 40x. It can be useful to give you a quick snapshot of your sequencing run. I personally do not put much stock in it as have found it to be misleading. What platform are you using and do you have linux, windows, or mac? I am not in the office now but would use bedtools to give the per base coverage, and awk to further process (combine and average all bases per amplicon, identify bases under desired reads, etc).Comment
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