Bedtools shift in a defined chromosomal position

Question

[ste.lu]

Hi All!

Do you know if there is a way to use bedtools shift tool in a defined chromosomal postions. In other words, shift +10 bp only the regions that are on chr1 in beteween 1 and 10000.

E.g:

chr1 10 100

chr1 20000 21000

bedtools shift -s 10 -chr_reg chr1:1-10000

chr1 20 110

chr1 20000 21000

Thanks!

Answer 1

[Pierre Lindenbaum]

extract the regions that are not in " chr1:1-10000"

run bedtools in chr1:1-10000

concatenate both files.