Question: A question about "Call differential binding events"
gravatar for mikysyc2016
7 months ago by
mikysyc201630 wrote:

Hi all, I read this blog But I have a question about it.

$ macs2 bdgdiff --t1 cond1_treat_pileup.bdg --c1 cond1_control_lambda.bdg --t2 cond2_treat_pileup.bdg\ --c2 cond2_control_lambda.bdg --d1 12914669 --d2 14444786 -g 60 -l 120 --o-prefix diff_c1_vs_c2

what is the meaning of -g 60 and -l 120 ? Thanks,

tf chip-seq • 346 views
ADD COMMENTlink modified 7 months ago by Kevin Blighe37k • written 7 months ago by mikysyc201630
gravatar for Kevin Blighe
7 months ago by
Kevin Blighe37k
Republic of Ireland
Kevin Blighe37k wrote:

Dear mikysyc2016, -l (--min-length) and -g (--max-gap) relate to the minimum peak size and the maximum distance between statistically significant peaks for the purposes of merging these into a single peak, respectively.

You can access the help pages by executing the following macs2 bdgdiff -h:

  -l MINLEN, --min-len MINLEN
                        Minimum length of differential region. Try bigger
                        value to remove small regions. DEFAULT: 200
  -g MAXGAP, --max-gap MAXGAP
                        Maximum gap to merge nearby differential regions.
                        Consider a wider gap for broad marks. Maximum gap
                        should be smaller than minimum length (-g). DEFAULT:


ADD COMMENTlink written 7 months ago by Kevin Blighe37k

Hi Kevin, If I use -l = fragment length i used as callpeaks and use -g as 100. i get 11294 peaks in common.bed and get 4692 peaks in con1.bed and get 2174 peaks in con2.bed. But I get 18347 peaks in con1 narrow.peaks and get 31410 peaks in con2 narrow.peaks. SO 11294+4692<18347 and 11294+2174<31410? do you think i need to change -g ?or I need to change peak length in narrow.peak as same as 200 then do diffpeak? Because the peak length is different after i use macs2 to do peak calling. Miky

ADD REPLYlink written 7 months ago by mikysyc201630

Have you checked some regions that you know should definitely be peaks? - how do the look? Yes, it is possible to refine your analysis by modifying the parameters but you should always have some sort of 'positive control' peaks that you know should exist (and negatives), which can help to guide you. In the past, I spent months going back and forth with different parameters for both MACS and HOMER, but nothing could ever get it exactly right (we tried every possible combination of values...).

ADD REPLYlink written 7 months ago by Kevin Blighe37k

Hi, I use homer to do the process and also use its merge peak parameter. I use IGV to see the specific and overlap peaks, as you mentioned, I think some of the specific peak is real weak( some look like real), do not look like real peak for me. Do you have any suggestion about how to choose the real specifc peaks? Thanks in advance.

ADD REPLYlink written 7 months ago by mikysyc201630

Well, what is your experiment? - it is a transcription factor or some other type of marker?

ADD REPLYlink written 7 months ago by Kevin Blighe37k

I did two TF ChIP-seq. And both of them express in same tissue. I want to t compare their binding sites( overlapped and specific).

ADD REPLYlink written 7 months ago by mikysyc201630

Okay, there should be previous literature that states the binding regions for these TFs. You could overlap your regions with the previous identified regions, or indeed just check that the binding motifs at your identified peaks match the expected binding motifs for your TFs. HOMER provides some functions for motif analysis

ADD REPLYlink written 7 months ago by Kevin Blighe37k
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