Question: bedtools shuffle with adjustment of GC ratio
2
gravatar for Shicheng Guo
3.4 years ago by
Shicheng Guo8.3k
Shicheng Guo8.3k 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.

ADD COMMENTlink modified 3.4 years ago by ivivek_ngs5.0k • written 3.4 years ago by Shicheng Guo8.3k
0
gravatar for ivivek_ngs
3.4 years ago by
ivivek_ngs5.0k
Seattle,WA, USA
ivivek_ngs5.0k 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 COMMENTlink modified 3.4 years ago • written 3.4 years ago by ivivek_ngs5.0k
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