Question: macs 1.4 (negative) peaks
gravatar for fabrizio.frasca
3.3 years ago by
fabrizio.frasca0 wrote:

Hi everyone!

I am using macs 1.4 to perform peak calling on a gata1 transcription factor ChIP-Seq experiment. It's just a didactic exercise. I got in output both the two files: gata1_peaks.xls and gata1_negative_peaks.xls. I know that negative peaks are called by swapping the treatment with the control and that they are to be considered as false positive peaks, but still I cannot figure out the rationale behind this. I mean: regions in gata1_negative_peaks.xls are not present in gata1_peaks.xls, so how are they supposed to be handled? What is the real information negative peaks bring about?

Is it the case that regions in gata1_peaks.xls are only the ones corresponding to peaks which are not negatively called?

The question arose from the need to evaluate an average overall FDR. I thought I could compute an empirical proxy as the ratio between the false positive peaks found and the overall number of peaks called. Then I wondered whether gata1_peaks.xls contains all the peaks called or only the 'true positves'. In the former case I could evaluate the overall FDR as (number of regions is gata1_negative_peaks.xls) / (number of regions in gata1_peaks.xls), while in the latter case I should do like (number of regions is gata1_negative_peaks.xls) / (number of regions in gata1_peaks.xls – number of regions is gata1_negative_peaks.xls).

Could someone please help me?

chip-seq macs • 1.4k views
ADD COMMENTlink modified 2.9 years ago by Biostar ♦♦ 20 • written 3.3 years ago by fabrizio.frasca0

The developers of MACS appear to have dealt with this issue in MACS2. Please see the response by the developer here:

Have you tried MACS2 to see what you get?

ADD REPLYlink written 2.9 years ago by Kevin Blighe63k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1486 users visited in the last hour