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jsh58 / Genrich

Detecting sites of genomic enrichment
MIT License
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Genrich peak calls with and without control sample #28

Closed codingforwork closed 4 years ago

codingforwork commented 4 years ago

Hi,

I was wondering how the normalization works if you only input experimental or only input control file for peak calling?

My goal is to look at them separately and see what is enriched in control and experimental samples. But I also want to look at differential peaks between them.

What would you recommend for how about I go about doing this analysis?

Thank you.

jsh58 commented 4 years ago

Thanks for the question.

First of all, Genrich requires an experimental input, so you would need to specify the input control file as the "experimental input" for the second run.

For downstream analysis, I recommend you look into bedtools and the answer to #19.

codingforwork commented 4 years ago

Okay, got it. Thank you.