closestBed

Reference

Similar to intersect, closest searches for overlapping features in A and B. In the event that no feature in B overlaps the current feature in A, closest will report the nearest (that is, least genomic distance from the start or end of A) feature in B. For example, one might want to find which is the closest gene to a significant GWAS polymorphism. Note that closest will report an overlapping feature as the closest—that is, it does not restrict to closest non-overlapping feature. The following iconic “cheatsheet” summarizes the funcitonality available through the various optyions provided by the closest tool.

Category

Genomic Interval Manipulation

Usage

closestBed [OPTIONS] -a -b

Manual

-s    Require same strandedness. That is, find the closest feature in B that overlaps A on the _same_ strand. By default, overlaps are reported without respect to strand.
-S    Require opposite strandedness. That is, find the closest featurein B that overlaps A on the _opposite_ strand. By default, overlaps are reported without respect to strand.
-d    In addition to the closest feature in B, report its distance to A as an extra column. The reported distance for overlapping features will be 0.
-D    

Like -d, report the closest feature in B, and its distance to A as an extra column. However unlike -d, use negative distances to report upstream features.
The options for defining which orientation is “upstream” are:
- ref Report distance with respect to the reference genome.
B features with a lower (start, stop) are upstream
- a Report distance with respect to A.
When A is on the - strand, “upstream” means B has a
higher (start,stop).
- b Report distance with respect to B.
When B is on the - strand, “upstream” means A has a
higher (start,stop).

-io    Ignore features in B that overlap A. That is, we want close, yet not touching features only.
-iu    Ignore features in B that are upstream of features in A. This option requires -D and follows its orientation rules for determining what is “upstream”.
-id    Ignore features in B that are downstream of features in A. This option requires -D and follows its orientation rules for determining what is “downstream”.
-fu    Choose first from features in B that are upstream of features in A. This option requires -D and follows its orientation rules for determining what is “upstream”.
-fd    Choose first from features in B that are downstream of features in A. This option requires -D and follows its orientation rules for determining what is “downstream”.
-t    
Specify how ties for closest feature should be handled. This occurs when two features in B have exactly the same “closeness” with A. By default, all such features in B are reported.
Here are all the options:
- all Report all ties (default).
- first Report the first tie that occurred in the B file.
- last Report the last tie that occurred in the B file.

-mdb    
Specifiy how multiple databases should be resolved.
- each Report closest records for each database (default).
- all Report closest records among all databases.

-k    Report the k closest hits. Default is 1. If tieMode = “all”, all ties will still be reported.
-names    When using multiple databases (-b), provide an alias for each that will appear instead of a fileId when also printing the DB record.
-filenames    When using multiple databases (-b), show each complete filename instead of a fileId when also printing the DB record.
-N    Require that the query and the closest hit have different names. For BED, the 4th column is compared.
-header    Print the header from the A file prior to results.

Share your experience or ask a question