I'm trying to determine the significance of eCLIP (similar to ChIP-seq, but RNA) peak overlaps.
I have used bedtools intersect to find how many overlaps there are between two bed files.
bedtools intersect -u -a file1.bed -b file2.bed -wa | wc -l
I thought about using bedtools fisher with the following command.
bedtools fisher -a file1.bed -b file2.bed -g genomeFile.bed
however, I'm getting inflated overlaps compared to bedtools intersect. If I take out the
-u option in bedtools intersect, I get the same amount of overlaps. I see no option in the bedtools fisher documentation to replicate
-u, which does the following:
"Write original A entry once if any overlaps found in B. In other words, just report the fact at least one overlap was found in B. Restricted by -f and -r."
Am I doing something wrong here? Should I shuffle the bed file?