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3 questions about code usage (white list and bioreplicates) #44

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sdjebali opened this issue Dec 1, 2020 · 1 comment

sdjebali commented Dec 1, 2020

Dear all,

Thanks for the nice method and associated code.

This is not really an issue but some general questions about the usage of the code.

can the white list file present here
example_chr22/reference/RefSeqCurated.170308.bed.CollapsedGeneBounds.chr22.bed
be used for any cell line, or is it specifically made for K562?
is it necessary or just recommended to use a white list file in the whole process? what are the advantages and drawbacks?
for H3K27ac data, do you recommend to use several bioreplicates whenever possible?

Best,

Collaborator

thouis commented Dec 10, 2020

@engreitz @jnasser3 - can you address the whitelist questions?

For 3, yes, replicates are almost always better.

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