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

0

Entering edit mode

3.1 years ago

Aspire ▴ 300

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 • 825 views

ADD COMMENT • link 3.1 years ago by Aspire ▴ 300

2

Entering edit mode

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 3.1 years ago by ATpoint 81k

0

Entering edit mode

The data is from an antibody to Nup107.

ADD REPLY • link 3.1 years ago by Aspire ▴ 300

1

Entering edit mode

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 3.1 years ago by ATpoint 81k

Login before adding your answer.