Bedtools accepts files with formats like 'chr start end name score strand'
However, is it possible to take these columns into account (e.g name column) when using bedtools intersect or bedtools merge.
For example I have a bed file like so, with a 'name' column for transposable elements
scaffold_1 913038 914038 DNA_transposon scaffold_1 925018 926018 LTR
scaffold_1 1026586 1027586 Mariner scaffold_1 925211 935660 DNA_transposon scaffold_1 925880 926300 LTR
but I would only like bedtools to intersect the 2nd line from FileA with the 3rd line from FileB, ignoring the 2nd line in FileB because it has "DNA_transposon" and not "LTR" in column4.
I can't find something like this in the manual file for bedtools. Knowing how to do it in bedtools would be helpful because it has the option to compare one bed file with many others (options -a and -b), in addition to many other options.