Thanks Ian, I have one more doubt. I have run chip-seq experiments on mouse samples and did peak calling using macs2 by the following command. pol1_1.fastq is the control sample and pu1_1.fastq is the chip sample.
macs2 callpeak -t pu1_1.fastq_trim.gz_A1.bam -c pol1_1.fastq_trim.gz_M1.bam -n pu1_1.fastq_trim.gz_A1.bam_macs2 -f BAM -g mm -B -q 0.01 --nomodel
It generated pu1_1.fastq_trim.gz_A1.bam_macs2.xls file. but all the fold enrichment values were positive. I couldnt find any negative values. what is the reason?
What do you think it means?
In order to motivate people to answer, provide details on what you are working on, what you have done so far and what your view on the matter is, as Devon already suggested.