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  • 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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