Question: Empty peaks after MACS2 (Galaxy Version using galaxy
gravatar for satishedu
2.3 years ago by
satishedu0 wrote:


I am working on Chipseq and have Followed the pipeline till macs2 where I get results as empty for few of my samples while other samples shows peaks.

ChipSeq samples(fastq) - FastQ Groomer - Bowtie2 (ref hg38) - MACS2 Callpeak(q = 0.05) . This has resulted in empty peaks.bed file for 8 samples out of 21. 

After a preliminary online search found few opinions and hence for the empty samples I have tried again a rerun with a threshold of q=0.1 as well as q = 0.8 but resulted in  same EMPTY peaks.

What could be the main reason for an empty peaks.bed file?


Below is what my empty peak.bed file contains(26 lines of comments)

# This file is generated by MACS version
# Command line: callpeak --name MACS2 -t /home/galaxy/galaxy-dist/database/files/066/dataset_66117.dat -c /home/galaxy/galaxy-dist/database/files/066/dataset_66118.dat --format=BAM --gsize 2451960000 --bw=300 --bdg --qvalue 0.8
# name = MACS2
# format = BAM
# ChIP-seq file = ['/home/galaxy/galaxy-dist/database/files/066/dataset_66117.dat']
# control file = ['/home/galaxy/galaxy-dist/database/files/066/dataset_66118.dat']
# effective genome size = 2.45e+09
# band width = 300
# model fold = [5, 50]
# qvalue cutoff = 8.00e-01
# 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 50 bps
# total tags in treatment: 42550570
# tags after filtering in treatment: 41655367
# maximum duplicate tags at the same position in treatment = 1
# Redundant rate in treatment: 0.02
# total tags in control: 35719666
# tags after filtering in control: 35035557
# maximum duplicate tags at the same position in control = 1
# Redundant rate in control: 0.02
# d = 49
# alternative fragment length(s) may be 49,280,528,592 bps



galaxy macs2 • 948 views
ADD COMMENTlink modified 2.3 years ago by Jennifer Hillman Jackson25k • written 2.3 years ago by satishedu0
gravatar for Jennifer Hillman Jackson
2.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


It could be that the treatment and control do not have significant differences to report with the given parameters. Maybe visualize a few regions, perhaps along with an annotation track, to understand the content better?

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.3 years ago by Jennifer Hillman Jackson25k
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