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tbischler / PEAKachu

Peak calling tool for CLIP-seq data
ISC License
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Controls or inputs? #13

Open hepcat72 opened 5 years ago

hepcat72 commented 5 years ago

I have CLIP-Seq samples with controls. The controls went through the same processing except the controls didn't have antibodies on the beads. (I didn't design the experiment incidentally). There was thus 10x less data off of the control runs. Is there anything I should know about using these controls with PEAKachu?

PatrickRWright commented 5 years ago

If you use the DESeq2 thread of the tool (PEAKachu) I suggest you have a closer look into what the significance of such sample size differences may be for DESeq2.

hepcat72 commented 5 years ago

Thanks. Are there any memory requirement guidelines for PEAKachu?

PatrickRWright commented 5 years ago

I am not an expert on the implementation so unfortunately I can't say.