Question: Error when using Bedtools fisher on sorted bed files
gravatar for ApoorvaB
3.6 years ago by
United States
ApoorvaB230 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 • 2.0k views
ADD COMMENTlink written 3.6 years ago by ApoorvaB230

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

ADD REPLYlink written 3.5 years ago by Fidel1.9k
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