I am confused with the --broad-cutoff option in macs2. In the manual, it said that --broad-cutoff is cutoff for broad region. This option is not available unless --broad is set. If -p is set, this is a pvalue cutoff, otherwise, it's a qvalue cutoff. DEFAULT: 0.1
If I understand it correctly, if I only set the --broad-cutoff 0.01, the cutoff will filter out broad peak with q-value > 0.01. However, when I processing a histone modification ChIP-seq data, I got some result with q-value > 0.01 [-log10(qvalue) <2].
Here is the result file.
# This file is generated by MACS version 18.104.22.16850731 # Command line: callpeak -t /mouseAnalysis/data/align/CYJ-1_dedup.bam -c /mouseAnalysis/data/align/CYJ-1i_dedup.bam -f BAM -n CYJ-1_CYJ-1i_macs.tmp -g mm -B --broad --broad-cutoff 0.01 --fix-bimodal --nomodel --extsize=270 --outdir /mouseAnalysis/data/peakCall/ # ARGUMENTS LIST: # name = CYJ-1_CYJ-1i_macs.tmp # format = BAM # ChIP-seq file = ['/mouseAnalysis/data/align/CYJ-1_dedup.bam'] # control file = ['/mouseAnalysis/data/align/CYJ-1i_dedup.bam'] # effective genome size = 1.87e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff for narrow/strong regions = 5.00e-02 # qvalue cutoff for broad/weak regions = 1.00e-02 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 1000 bps and 10000 bps # Broad region calling is on # tag size is determined as 49 bps # total tags in treatment: 8279763 # tags after filtering in treatment: 8279763 # maximum duplicate tags at the same position in treatment = 1 # Redundant rate in treatment: 0.00 # total tags in control: 9357359 # tags after filtering in control: 9357359 # maximum duplicate tags at the same position in control = 1 # Redundant rate in control: 0.00 # d = 270 chr start end length pileup -log10(pvalue) fold_enrichment -log10(qvalue) name chr11 3132147 3132916 770 46.55 5.11039 1.29032 1.91284 CYJ-1_CYJ-1i_macs.tmp_peak_1 chr11 3168653 3168940 288 39.21 4.37530 1.18763 1.48268 CYJ-1_CYJ-1i_macs.tmp_peak_2 chr11 3193021 3193581 561 46.44 5.97673 1.34145 2.72753 CYJ-1_CYJ-1i_macs.tmp_peak_3
My questions are:
Do I understand the --broad-cutoff correctly? Why the filter doesn't work?