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bedtools shuffle with adjustment of GC ratio

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.

bedtools shuffle sampling gc contents
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updated by ivivek_ngs ivivek_ngs • written by Shicheng Guo Shicheng Guo

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.

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written by zekexu • zekexu

1 answer

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

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written by ivivek_ngs ivivek_ngs

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