Question: Bedtools fisher result
gravatar for sxf710
10 months ago by
sxf7100 wrote:

I would like to run a fishers exact test using bedtools fisher. I have two files to test the overlap, and a genome file. However, the result does not give me an odds ratio, and the number of possible intervals is the same number as the number of query intervals. I have ran the same code with different files and it works fine, so I am not sure what is going on here. See the result below:

# Number of query intervals: 962714
# Number of db intervals: 18661
# Number of overlaps: 516254
# Number of possible intervals (estimated): 962714
# phyper(516254 - 1, 962714, 962714 - 962714, 18661, lower.tail=F)
# Contingency Table Of Counts
#                  |  in -b           | not in -b    |
#     in -a        | 516254           | 446460       |
# not in -a        | 0                | 0            |
# p-values for fisher's exact test
left    right   two-tail    ratio
1   1   1   -nan

How would one interpret this result and could there be an issue with the files?

fisher bedtools genome • 460 views
ADD COMMENTlink written 10 months ago by sxf7100

The strange thing is that the counts for "not in -a" (second row of the 2 by 2 contingency table) are zero. I would suggest to check this issue

ADD REPLYlink written 10 months ago by Fabio Marroni2.5k
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