Question: what is bedtools closest distance to gene?
0
gravatar for Medhat
3.5 years ago by
Medhat8.1k
Texas
Medhat8.1k wrote:

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

 

sequencing next-gen gene • 1.2k views
ADD COMMENTlink modified 3.5 years ago by Devon Ryan88k • written 3.5 years ago by Medhat8.1k
1
gravatar for Devon Ryan
3.5 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

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).

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Devon Ryan88k

But can I use predefined distance? 

ADD REPLYlink written 3.5 years ago by Medhat8.1k

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.

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by Devon Ryan88k

exactly giving some range to search 

ADD REPLYlink written 3.5 years ago by Medhat8.1k
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