Question: Bed file data Vs HOMER output
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gravatar for pinky_pinkpinky
5.2 years ago by
India
pinky_pinkpinky50 wrote:

Dear Users,

I have a very fundamental doubt in chip-seq analysis.

We get the chromosome, poistion and read count information from the bed files for Input and IP samples and based on the position I generate the peak plots.

Using HOMER, we use the script findPeaks and get the peak information as well. How do we compare this result with the plots generated from the read count information?

Is it the genomic positions of the chromosomes which we get through HOMER findpeak output needs to be compared with the peak plot generated based on read count or something else? Is this correct to decide the enriched peaks or something else?

Any suggestions?

Thanks

Abhi

chip-seq homer • 1.6k views
ADD COMMENTlink modified 4.2 years ago by Biostar ♦♦ 20 • written 5.2 years ago by pinky_pinkpinky50
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