what is bedtools closest distance to gene?

Question

[Medhat]

As declared in the question, what is the calculated distance by the program to count that some sequence is close to gene?

Answer 1

[Devon Ryan]

It's just using the genomic distance, so from the edge(s) of whatever feature you're interested in to the nearest edge of the next gene (possibly taking strand into account and/or ignoring any overlapping features, depending on the settings you use).

[Medhat]

But can I use predefined distance?

[Devon Ryan]

You mean like asking for the closest within a certain distance range (i.e., not the closest per se but perhaps that closest that's at least 10kb away)? I don't think there's a parameter for that.

[Medhat]

exactly giving some range to search