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Question: bedtools shuffle with adjustment of GC ratio
2
gravatar for Shicheng Guo
3.9 years ago by
Shicheng Guo • 8.5k
Shicheng Guo • 8.5k wrote:

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.

gc contents bedtools shuffle sampling • 1.2k views
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modified 3.9 years ago by ivivek_ngs • 5.1k • written 3.9 years ago by Shicheng Guo • 8.5k

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.

ADD REPLY • link modified 6 weeks ago • written 6 weeks ago by zekexu • 0
0
gravatar for ivivek_ngs
3.9 years ago by
ivivek_ngs • 5.1k
Seattle,WA, USA
ivivek_ngs • 5.1k wrote:

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
ADD COMMENT • link modified 3.9 years ago • written 3.9 years ago by ivivek_ngs • 5.1k
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