bedtools: get name column of alignment file A I'm using the coverage function of bedtools to check whether a certain set of regions (file B) has any overlap with known regions of epigenetic markers (file A). When that is the case, I want to access the name of that marker, which is given as the third column (name) in file A. 

However, when I run bedtools coverage -a fileA.bed -b fileB.bed, I only get the columns of file B as an output, together with the overlap fraction. Is there a built-in way of accessing also the columns of the file A to which I aligned, or an easy way of cross-referencing to it?
I would recommend using bedtools intersect for that type of comparison.  This will allow you to see the specific segments that overlap.  bedtools coverage is used more for determining how many things cover a region but not which ones.  

The documentation linked above will provide a much better desciption of intersect than I would be able to in this post but I would recommend using the -loj or -u depending on what you want.

-loj    Perform a “left outer join”. That is, for each feature in A report each overlap with B. If no overlaps are found, report a NULL feature for B.

-u  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.