Bedtools fisher test error

Question

[brisbio]

I want to run the bedtools fisher command. For this I first sort my files using sort -k1,1 -k2,2n.

When I go to run the fisher test:

bedtools fisher -a a_sorted.txt -b b_sorted.txt -g rn6_chrom_sorted.txt

It says

exiting integer conversion of a string “282763074

What am I doing wrong? (The 282763074 is the length of chr 1 in my genome file).

Answer 1

[Pierre Lindenbaum]

check you don't have any column with a blank character (space, crlf, ... ) near the word '282763074'.

[brisbio]

Thank you! When I used sed to remove crlf and then performed the fisher test it worked!