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!