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ENCODE-DCC / chip-seq-pipeline2

ENCODE ChIP-seq pipeline
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MACS2 Peaks Cap #202

Closed YogiOnBioinformatics closed 3 years ago

YogiOnBioinformatics commented 3 years ago

I had a question about the number of peaks taken from MACS2. Why is the number of peaks capped at 500,000 for this pipeline vs 300,000 for the ENCODE-DCC ATAC-Seq Pipeline?

It would be very useful for me to know since I plan to analyze ChIP-Seq and ATAC-Seq data from the same biological samples soon. Please let me know if this makes sense.

akundaje commented 3 years ago

No particular reason other than that certain types of histone marks (ChIP) can often have a larger number of narrow peaks than ATAC/DNase.

-Anshul.

On Mon, Dec 7, 2020 at 7:40 AM Yogindra Raghav notifications@github.com wrote:

I had a question about the number of peaks taken from MACS2. Why is the number of peaks capped at 500,000 for this pipeline vs 300,000 for the ENCODE-DCC ATAC-Seq Pipeline?

It would be very useful for me to know since I plan to analyze ChIP-Seq and ATAC-Seq data from the same biological samples soon. Please let me know if this makes sense.

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YogiOnBioinformatics commented 3 years ago

Perfect! :) Thanks so much as always for the quick reply.