Bedtools Fisher Genome File
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12 months ago
megannj ▴ 10

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.

bedtools fisher genome overlap chipseq • 337 views