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 18.104.22.16851222
# 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
# ARGUMENTS LIST:
# 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