How can the assumption of a broad/narrow peak be checked?

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3.8 years ago

Aspire ▴ 370

With ChIP-Seq data, macs2 needs to be informed whether to call narrow peaks, or broad (essentially uniting smaller peaks, as far as I understand).

Is there a way to check from the data itself which type of peak is more suitable? E.g. if I am not sure what type of peak to expect.

macs2 ChIP-Seq • 988 views

ADD COMMENT • link 3.8 years ago by Aspire ▴ 370

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What did you ChIP? You can also look at the browser tracks and see by eye whether peaks are narrow or stretch over several tens of kb.

ADD REPLY • link 3.8 years ago by ATpoint 86k

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The data is from an antibody to Nup107.

ADD REPLY • link 3.8 years ago by Aspire ▴ 370

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I have not worked with this protein so far, as said I would simply check the browser tracks. I would guess it is a narrow peak, but this is only a gut feeling.

ADD REPLY • link 3.8 years ago by ATpoint 86k

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