I have converted a gene annotation file using
bedtools and used another bed file containing regions under selective sweeps. My goal is the find how many genes are inside the interval of the selective sweep regions.
I have a converted gene annotation file called
gene_annot.bed and another file containing intervals in each scaffold called
sweep_interval.bed. I first sorted both the annotation and the selective sweep interval files in
bedtools and then used the following code to find how many genes are overlapping with the intervals.
bedtools intersect -a gene_annot.bed -b sweep_interval.bed -wa > results.txt
Using this code, I got 915 genes. But if I used the following code:
bedtools intersect -a gene_annot.bed -b sweep_interval.bed -u -wa > results_1.txt
Then I got 905 genes.
Can you please tell me if the code I am using especially
-b is right and if should I use the
-u option or not?