Question: Extending BED intervals
0
gravatar for rbronste
3 months ago by
rbronste230
rbronste230 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 • 174 views
ADD COMMENTlink modified 3 months ago by Alex Reynolds27k • written 3 months ago by rbronste230
2
gravatar for Alex Reynolds
3 months ago by
Alex Reynolds27k
Seattle, WA USA
Alex Reynolds27k 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 3 months ago • written 3 months ago by Alex Reynolds27k
1
gravatar for Pierre Lindenbaum
3 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum116k 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 3 months ago by Pierre Lindenbaum116k
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