Hi y'all, I'm new to BEDtools and this type of data analysis in general, and I'm having a lot of trouble getting going.
I have two excel files that I saved as .txt files and then changed to .bed files and put in the Bedtools folder I'm using. They each have a column for chromosome number, start site, and end site. These are listed at the top but are commented out with #.
I can use bedtools and follow along with the tutorial and intersect will work. However, when I try to use my own files ("bedtools intersect -a EuarchCons6.bed -b PbxEmx6.bed | head -5") the terminal takes a minute to load and then displays nothing, as if there's no overlap or something, but I'm sure there is. I even created a test file with made up sequences that I knew overlapped with the first several regions in one of the files and it returned nothing.
I'm sure I'm probably missing something simple here, but if anyone could help me understand why intersect doesn't appear to be working that'd be really helpful. Thanks so much.