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Question: Does CRISPRSEEK work on previously unknown genomes?
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gravatar for yhuang2
9 months ago by
yhuang20
yhuang20 wrote:

What genomes are supported by CRISPRSEEK?  Is it possible to analyze novel genomes?  If so, what are the requirements (format of genome file, etc) for the new genome?

 

ADD COMMENTlink modified 9 months ago by Julie Zhu3.8k • written 9 months ago by yhuang20
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gravatar for Julie Zhu
9 months ago by
Julie Zhu3.8k
United States
Julie Zhu3.8k wrote:

Yanmei,

Thanks for taking time to post the question! https://bioconductor.org/packages/3.5/BiocViews.html#___BSgenome lists BSgenomes that can be directly used as input to CRISPRseek .

For detailed information on how to use the package, please read the user guide at http://bioconductor.org/packages/devel/bioc/vignettes/CRISPRseek/inst/doc/CRISPRseek.pdf and the supplementary file in the following publication

 Zhu LJ, Holmes BR, Aronin N and Brodsky MH (2014). “CRISPRseek: A Bioconductor Package to Identify Target-Specific Guide RNAs for CRISPR-Cas9 Genome-Editing Systems.” PLoS one, 9(9). http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4172692/.

To design guides without available BSgenome, please refer to this post at  CRISPRseek with genome not available in BSgenome. It also talks about analyzing data for novel genome using compare2Sequences function  https://github.com/Bioconductor-mirror/CRISPRseek/blob/master/man/compare2Sequences.Rd.

​Best regards,

Julie

ADD COMMENTlink written 9 months ago by Julie Zhu3.8k

Thanks Julie.  This is very helpful. 

ADD REPLYlink written 9 months ago by yhuang20
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