Question: ChIP-seq: Why MACS doesn't apply tag shifting to the control sample?
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gravatar for salamandra
10 months ago by
salamandra170
salamandra170 wrote:

If I understand right, MACS shifts chip-seq tags of a fragment into 3┬┤end because the tags are just small sequences in the extremes of the fragment. But why does it only apply to the ChIP sample and not to the control samples (input DNA)? Or paired-end sequencing isn't done in control samples?

Ref: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2008-9-9-r137

chip-seq • 378 views
ADD COMMENTlink modified 10 months ago by ghostforever.shi20 • written 10 months ago by salamandra170
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gravatar for ghostforever.shi
10 months ago by
ghostforever.shi20 wrote:

With a control, MACS will do the peak calling in both sample(test and input) and count the FDR according to the result of two samples' peak calling, which means, in my opinion, tag shifting will be applied to both samples.

ADD COMMENTlink written 10 months ago by ghostforever.shi20
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