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Old 01-26-2010, 07:51 AM   #1
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Location: chicago

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Default Coverage for exon

Hi everyone,

I want to calculate coverage for exon sequences using 454AlignmentInfo.tsv file. I have a bed file of exons. So to calculate coverage is it enough if i average the unqiue depth of every base in the exon to get total coverage for that exon ? or should I use average of total depth for each base ?

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Old 02-02-2010, 10:35 AM   #2
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Unique depth is more correct, as Total depth includes the duplicate reads. These are (usually) the results of two beads ending up in the same (micro)reaction during emPCR, resulting in them obtaining the exact same ssDNA strand, resulting in basically the same flowpattern.
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