BedOverlapName: Difference between revisions

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Add overlapping bedname from second bed:
<pre>
<pre>
#!/bin/bash
#!/bin/bash
PREFIX=$3
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}'
overlapSelect $1 $2 -mergeOutput stdout -dropped=stdout|  cut -f 1,2,3,4,8 \
    | gawk '{OFS="\t";print $1,$2,$3,$4",'$PREFIX'"$5}'
</pre>
</pre>
example:
<pre>
  bedOverlapName randomFeatures.bed geneAnnotation.bed EXON_  |
  bedOverlapName stdin conservedRegions.bed CR_ |
  bedOverlapName stdin UTRs UTR_
</pre>
will annotate the bed names with various additional information, each seperated by a comma


[[Category:User Developed Scripts]]
[[Category:User Developed Scripts]]

Latest revision as of 21:41, 26 October 2006

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