Question: Error when using Bedtools fisher on sorted bed files
1
gravatar for Apoorva
4.4 years ago by
Apoorva250
United States
Apoorva250 wrote:

Hi Everyone,

I am doing a ChIP-Seq analysis on a small dataset of 6 samples (Wild-type and knockout having 3 replicates each). I wanted to run a Fisher exact test using bedtools. My bed files are all sorted. But I am getting this error.

Error: Sorted input specified, but the file /Users/xxx/narrowPeak/531-sorted.bed has the following record with a different sort order than the genomeFile /Applications/bedtools2/genomes/mouse.mm9.genome

What does this mean and how do I fix this ?

Thank you

chip-seq fisher test bedtools • 2.5k views
ADD COMMENTlink written 4.4 years ago by Apoorva250
1

check that the order of the chromosome names and the order of your sort is the same as in the genome.

ADD REPLYlink modified 5 months ago by RamRS27k • written 4.4 years ago by Fidel1.9k
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