Question: Empty output from MACS2 when using control
0
gravatar for lm687
24 months ago by
lm68740
lm68740 wrote:

Hello,

I have been trying to perform peak calling with MACS2. I get an output when I don't use a control file, but blank files when I do. I'm reproducing someone else's results so there shouldn't be a problem with the input (I have only aligned the reads to the genome using BWA). I am running it with default parameters

macs2 callpeak -t SRR001992.bam -c SRR001999.bam

and changing the cutoff -q still yields blank files. Does anyone know where the problem could be? Thank you!

chip-seq macs2 peak calling • 1.3k views
ADD COMMENTlink modified 4 months ago by macmath120 • written 24 months ago by lm68740
1

Can you maybe post the output of macs2?

Default params include -mfold 5 50, try lowering it to 2 50 maybe. In several datasets I cannot get any peaks with the default mfold. 

ADD REPLYlink written 24 months ago by rioualen220

Thank you, I have modified the parameters but I still get the same blank output. The files peaks.narrowPeak and summits.bed are empty. peaks.xls is:

# This file is generated by MACS version 2.1.0.20151222
# Command line: callpeak -t bwaSRR001992_sorted.bam -c bwaSRR001998_sorted.bam -m 2 50 -n macs2_with_control/bwaSRR001992_sorted.bam
# ARGUMENTS LIST:
# name = macs2_with_control/bwaSRR001992_sorted.bam
# format = AUTO
# ChIP-seq file = ['bwaSRR001992_sorted.bam']
# control file = ['bwaSRR001998_sorted.bam']
# effective genome size = 2.70e+09
# band width = 300
# model fold = [2, 50]
# qvalue cutoff = 5.00e-02
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off

# tag size is determined as 26 bps
# total tags in treatment: 4374226
# tags after filtering in treatment: 3824323
# maximum duplicate tags at the same position in treatment = 1
# Redundant rate in treatment: 0.13
# total tags in control: 4090488
# tags after filtering in control: 3608175
# maximum duplicate tags at the same position in control = 1
# Redundant rate in control: 0.12
# d = 131
# alternative fragment length(s) may be 131 bps

model.r contains vectors p, m, xcorr and x.

Thank you

ADD REPLYlink written 24 months ago by lm68740

Another try would be to load these files in the browser and to see how similar the profiles are, that could be an another reason.

ADD REPLYlink written 24 months ago by Sukhdeep Singh9.2k

thank you, I will do this. Does the amount of total tags in the control seem reasonable?

ADD REPLYlink modified 24 months ago • written 24 months ago by lm68740

This I think has no limits, depending upon how much was sequenced and how the data was pre-processed. But macs integrates a scaling option, so for most cases, you don't need to worry about that.

# Larger dataset will be scaled towards smaller dataset.

ADD REPLYlink modified 24 months ago • written 24 months ago by Sukhdeep Singh9.2k

thank you for the information!

ADD REPLYlink written 24 months ago by lm68740

If you like someone's answer and they satisfy you, you thank people by upvoting them on Q/A platforms and forums.
Good Luck!

ADD REPLYlink written 24 months ago by Sukhdeep Singh9.2k

How to solve this issue? I am having a similar problem.

ADD REPLYlink written 11 months ago by xiang-jiao.yang0
1
gravatar for Sukhdeep Singh
24 months ago by
Sukhdeep Singh9.2k
Netherlands
Sukhdeep Singh9.2k wrote:

Another user had this problem, from the Tao's answer

Can’t see any problem. Some guesses:

  1. qvalue cutoff is too high. Try lower it such as -q 0.1
  2. disk full
  3. chromosome names in ChIP file and control file are not consistent. e.g. ‘chr1’ in ChIP but ‘chromosome1’ in control
ADD COMMENTlink modified 24 months ago • written 24 months ago by Sukhdeep Singh9.2k

Thank you very much! Unfortunately, I don't think it can be either of these

ADD REPLYlink written 24 months ago by lm68740
0
gravatar for darsal2
20 months ago by
darsal20
Chicago, IL, USA. University of Illinois at Chicago
darsal20 wrote:

Did you ever figure out a solution? I am also having the same problem. All of my output files are empty... I'm running it using these parameters:

macs2 callpeak -t 4_D.bam -c 1_D.bam -g 2.5e8 -nomodel -n 4v1rep41_test -q 0.01

ADD COMMENTlink written 20 months ago by darsal20
0
gravatar for macmath
4 months ago by
macmath120
France
macmath120 wrote:

Could you check the parameter specifically based on the differences between regular peak vs broad peak

Example for regular peak calling: macs2 callpeak -t ChIP.bam -c Control.bam -f BAM -g hs -n test -B -q 0.01

Example for broad peak calling: macs2 callpeak -t ChIP.bam -c Control.bam --broad -g hs --broad-cutoff 0.1

ADD COMMENTlink written 4 months ago by macmath120
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