Question: Bedtools fisher result

0

sxf710 •

**0**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?

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

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