Hi, all. I'm trying to compare ChIP-seq peak lists of two transcription factors using bedtools fisher. My command is:
#bedtools fisher -a Factor1.bed -b Factor2.bed -g mm10.chrom.sizes
where the Factor1 and Factor2 files are both lists of peaks 101 bp in width. The mm10.chrom.sizes file contains the size of each chromosome in the mouse genome.
When I do this, I get the following:
# Number of query intervals: 27176 # Number of db intervals: 44018 # Number of overlaps: 25704 # Number of possible intervals (estimated): 13386626 # phyper(25704 - 1, 27176, 13386626 - 27176, 44018, lower.tail=F) # Contingency Table Of Counts #_________________________________________ # | in -b | not in -b | # in -a | 25704 | 1472 | # not in -a | 18314 | 13341136 | #_________________________________________ # p-values for fisher's exact test left right two-tail ratio 1 0 0 12720.451
Is this correct? I'm concerned I'm not using the correct background (-g) file since the possible intervals list is so high.