bedtools shuffle with adjustment of GC ratio

Question

[Shicheng Guo]

Hi All,

Is there any script which can be used for bedtools shuffle and can be applied to ‘GC' ratio control/adjustment ?

I want to random re-sampling same genomic regions with same length distribution and similar 'GC' contents.

Perl script will be preferred.

Thanks.

[zekexu]

Hi Dr. Guo,

Wondering if you have found a feasible solution? Or how to define the GC% range? I met the same question too.

Thank you for your time.

Answer 1

[ivivek_ngs]

I would encourage you to look in to the below links for coming up with a solution. There is a bash script which you can convert to perl script to be honest.

Picking random genomic positions

Perl script: generate pseudo-CDSs from intergenic region