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Old 09-10-2014, 08:17 AM   #6
Junior Member
Location: Denmark

Join Date: Aug 2011
Posts: 7

If your supervisor wants a p-value, then I have likely missed the point.

I originally assumed the aim was to ask a question like "does this sample have adequate coverage for my purposes?”. For the purpose of noting samples that might not have adequate coverage for downstream analysis, I think a set of coverage cutoffs for the various genes of interest, based on some lower limit you determine based on your knowledge of a “good” sample, would be a reasonable way forward.

To me, a p-value suggests questions more long the line of "does this sample have (any, some, all?) genes that have coverage that fall outside a range that constitutes the population of what are considered good samples?" That is a rather more complex question to approach.
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