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megannj 04-06-2020 10:28 AM

BedTools Fisher Question
 
Hi, All! I have a question about the usage of the bedtools fisher tool. I have posted elsewhere but have not received answers.

I am trying to determine the significance of ChIP-seq peak overlap. I have two files with peaks all 101 bp in width. I entered the following command:

Code:

bedtools fisher -a Factor1.bed -b Factor2.bed -g mm10.chrom.sizes
The file mm10.chrom.sizes contains each mouse chromosome and it's length. The output I received is:

Code:

# 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

This doesn't make sense to me. I feel that I am likely using the incorrect genome file, but am not sure what to use. Any advice?


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