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Why only read2 is used for peak calling? #43

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FionaMoon opened this issue Dec 7, 2023 · 0 comments

FionaMoon commented Dec 7, 2023

Hi developer,

As I ran eclip pipeline with pare-end data, I noticed that this pipeline only outputs the second read in each pair for use with peak caller.

According to eclip experiment, the crosslink site should be in read1, like this:

So, I wonder why we call peaks based on read2 but not read1?

Thank you in advance!

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