Question: ChIP-seq: Why MACS doesn't apply tag shifting to the control sample?
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gravatar for salamandra
3 months ago by
salamandra80
salamandra80 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 • 212 views
ADD COMMENTlink modified 12 weeks ago by ghostforever.shi20 • written 3 months ago by salamandra80
0
gravatar for ghostforever.shi
12 weeks 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 12 weeks ago by ghostforever.shi20
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