Question: Bedtools fisher test error
gravatar for emilyprice16
4 months ago by
emilyprice1620 wrote:

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).

fisher bedtools • 174 views
ADD COMMENTlink modified 4 months ago by Ram32k • written 4 months ago by emilyprice1620
gravatar for Pierre Lindenbaum
4 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum134k wrote:

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

ADD COMMENTlink written 4 months ago by Pierre Lindenbaum134k

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

ADD REPLYlink modified 4 months ago • written 4 months ago by emilyprice1620
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