I am analyzing a CLIP-Seq, and I have been working with Bedtools for about 2 months now, so I am still a novice. I recently created a series of windows around splice junctions, and I wanted to know how many CLIP tags were in each window. I created a window 50 bp surrounding a splice junction (25 on each side), and I used two different tools to look at the number of tags in this region.
First I used "intersect: intersect clip-tags on window," and my output was a list of 7,267 chromosome coordinates that I presume represent clip-tag regions that intersected with the window.
I also tried bedtools intersect-count (and count overlapping intervals in Galaxy; they gave the same result): Count how many clip-tags overlap window," and my output said that 12,866 clip tags overlapped this region.
I don't understand why these numbers are not the same. I just want to know how many clip tags overlap this bin, and what the difference is between these tools.
Thank you for your help,