Extending BED intervals

Question

[rbronste]

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!

Answer 1

[Alex Reynolds]

With bedops --range:

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

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

Answer 2

[Pierre Lindenbaum]

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);}'