Question: ChIP-Seq Read Counts
gravatar for teabonng
12 months ago by
teabonng20 wrote:

Hi Everyone,

I am very new to ChIP-Seq analysis, but i will be analyzing data from multiple studies. However, some ChIP seq studies do not have Input to compare the distribution of mapped reads, so I cannot do peak calling. In this case, is it common practice to simply get the normalized counts (like number of reads relative to library size) for each locus/gene and then compare these values?

Thank you very much.


chip-seq • 445 views
ADD COMMENTlink written 12 months ago by teabonng20
gravatar for ATpoint
12 months ago by
ATpoint21k wrote:

You can call peaks withput input control. MACS has that option, trying to assess the background by a local lambda, check the priginal paper for details.

ADD COMMENTlink written 12 months ago by ATpoint21k
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