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Old 04-06-2020, 10:28 AM   #1
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Default 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:

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:

# 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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bedtools, chip-seq analysis, fisher test

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