Question: What Parameters Do You Use With Findpeaks For Chip Seq Peak Calling?
gravatar for Stew
8.4 years ago by
Stew1.4k wrote:

I would like to use FindPeaks to call peaks on chIP-seq data, where I have an IP against a sequence specific transcription factor, using Input as control. I would appreciate any guidance as to which control methods, cutoff and FDR methods people are using.

I am currently running MACS and SWEMBL also, and though I get good agreement between these two, I do not get very good agreement with findPeaks.

Specific command line options or general guidance about use would be helpfil. I am using it on pre-filtered (on alignment score) BAM files.

chip-seq • 3.8k views
ADD COMMENTlink modified 5.7 years ago by Biostar ♦♦ 20 • written 8.4 years ago by Stew1.4k
gravatar for Dawe
8.4 years ago by
Dawe260 wrote:

Hi, I use FindPeaks (FP4) and MACS as well. My typical FP4 parameters are:

-disttype 1 200 -subpeaks 0.2 -duplicatefilter -bedgraph -autothreshold 0.95

I then filter .peaks file for p ≤ 0.01 (or less) and ht on the "auto_threshold" results

ADD COMMENTlink modified 8.4 years ago • written 8.4 years ago by Dawe260

That is very helpful thanks, not very different to what I as doing. What do you mean by filtering on "ht on the auto_threshold results" though?

ADD REPLYlink written 8.4 years ago by Stew1.4k

If you run FP4 with -auto_threshold [?] parameter, you'll notice a line in the log file that will tell you the min. height you should filter (per chromosome) to achieve a [?] confidence on your peaks. I've recently defaulted that flag to 0.99

ADD REPLYlink written 8.3 years ago by Dawe260

Great, thanks. I didn't know that part. I will take a look.

ADD REPLYlink written 8.3 years ago by Stew1.4k
gravatar for Husen
8.3 years ago by
Husen0 wrote:

I have a similar problem with FindPeaks, the bedgraph output is too big compare to output of other peak callers like MACS and Erange.

That is what I use: -aligner bed -dist_type 1 -duplicatefilter -bedgraph

Do you know if there is any option to get less peaks in the bedgraph output?

thanks for your help

ADD COMMENTlink written 8.3 years ago by Husen0

Hi Husen, I'm the author of FindPeaks, so I can tell you that there are a lot of options - but they're not bedgraph specific. The bedgraph option just dumps out the output in bedgraph format. You need to use the program options to filter the output, such as -minimum or even the -control or -compare options.

ADD REPLYlink written 8.3 years ago by apfejes160
gravatar for suman
6.3 years ago by
suman0 wrote:

Hi, I have a question regarding the -iterations and -landerwaterman options. I read that the landerwaterman options best with disttype 0 as it performs poorly with weighted (-disttype 1) distributions and the native/PET (-dist_type 3) distributions.

a)Is the value of integer following dist_type 0 the tag length like 26 reads or 36 reads that we provide in MACS ? b)Can i use both options together in a command ?


ADD COMMENTlink written 6.3 years ago by suman0
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