BedOverlapName

From genomewiki
Jump to navigationJump to search
The printable version is no longer supported and may have rendering errors. Please update your browser bookmarks and please use the default browser print function instead.

Add overlapping bedname from second bed:

#!/bin/bash
PREFIX=$3
overlapSelect $1 $2 -mergeOutput stdout -dropped=stdout|  cut -f 1,2,3,4,8 \
    | gawk '{OFS="\t";print $1,$2,$3,$4",'$PREFIX'"$5}'

example:

  bedOverlapName randomFeatures.bed geneAnnotation.bed EXON_  |
  bedOverlapName stdin conservedRegions.bed CR_ |
  bedOverlapName stdin UTRs UTR_

will annotate the bed names with various additional information, each seperated by a comma