Question: Extending BED intervals
0
gravatar for rbronste
7 months ago by
rbronste240
rbronste240 wrote:

Kind of a straightforward question, but what is a quick/simple method to take a bed file with an avg bp size of 350 and extend every interval by 325bp in each direction? Thanks!

interval bedops bed bedtools • 257 views
ADD COMMENTlink modified 7 months ago by Alex Reynolds28k • written 7 months ago by rbronste240
2
gravatar for Alex Reynolds
7 months ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

With bedops --range:

$ bedops --range 325 --everything in.bed > out.bed

https://bedops.readthedocs.io/en/latest/content/reference/set-operations/bedops.html

ADD COMMENTlink modified 7 months ago • written 7 months ago by Alex Reynolds28k
1
gravatar for Pierre Lindenbaum
7 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:

bedtools slop https://bedtools.readthedocs.io/en/latest/content/tools/slop.html

or awk

awk -F '\t' '{x=325;S=int($2)-x;printf("%s\t%d\t%d\n",$1,(S<0?0:S),int($3)+x);}'
ADD COMMENTlink written 7 months ago by Pierre Lindenbaum120k
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