macs callpeak q value cutoff 1 and 0.05 with different peak result
Hi，
I am using macs call peak, when I set q cutoff with 1 and 0.05, the results show a little different, set -q 1, found ~1500 peaks with q<0.05, but set "-q 0.05" only reported ~800 peaks, and there ~100 peaks which were not called by -q 1. All commands are same except for -q
What's reason about this issues?
Command I used:
macs2 callpeak -t ACTAACTGCT_ChIPMix53_bt2.bam -c TAGCTT_bt2.bam -f BAM -g 3.1e7 -n mix53 -B -q 1.00 --nomodel --extsize 147 --outdir peak_output1
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If I understood your question correctly, you are simply giving different FDR cutoffs for the statistical significance of the peaks called by the algorithm. Naturally, the more stringent you go with your FDR cutoff, the fewer peaks will be called.