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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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Avg coverage calculation #18

Closed ramaniak closed 9 years ago

ramaniak commented 9 years ago

Hello, thanks for the great tool...this is more of a question rather than an issue. I am using bamstat04 and everything works perfectly. I want to ensure that I am reading the calculations correctly and was therefore wondering if you could explain briefly how the avg coverage is calculated? Is this as follows: given 'N' reads of length 'L' mapping to a region of length 'R' with 100% of the region is covered the avg cov = N*L/R? or do you consider the coverage at each position? Thanks

lindenb commented 9 years ago

as you said, I only consider the coverage at each position.

ramaniak commented 9 years ago

Thanks