Question: CRISPRseek:::findgRNAs paired gRNAs with PAM inward orientation
0
gravatar for saba.parvez
4 months ago by
saba.parvez0 wrote:

I am using the CRISPRseek package to design paired gRNAs for nickase enzyme. I am interested in designing paired gRNAs in PAMin orientation. Is it possible to specify the orientation of the adjacent PAMsites in CRISPRseek such that the output yields paired gRNAs that are facing in PAMin orientation rather than PAMout orientation?

Note: In PAMin orientation the two adjacent PAMs on the sense and antisense strands face inwards towards each other (N21GG and CCN21) whereas in the PAMout orientation they face away from each other (CCN21 and N21GG)

Thank you

crisprseek paired grna • 108 views
ADD COMMENTlink modified 4 months ago by Julie Zhu4.0k • written 4 months ago by saba.parvez0
Answer: CRISPRseek:::findgRNAs paired gRNAs with PAM inward orientation
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gravatar for Julie Zhu
4 months ago by
Julie Zhu4.0k
United States
Julie Zhu4.0k wrote:

Saba,

Thanks for posting the question! I will add the functionality and let you know when it is done.

Best regards,

Julie

ADD COMMENTlink written 4 months ago by Julie Zhu4.0k

Thanks Dr. Zhu! I will wait for your response.

ADD REPLYlink written 4 months ago by saba.parvez0
Answer: CRISPRseek:::findgRNAs paired gRNAs with PAM inward orientation
0
gravatar for Julie Zhu
4 months ago by
Julie Zhu4.0k
United States
Julie Zhu4.0k wrote:

Saba,

Please download the newest version of CRISPRseek (Version: 1.25.2). To find paired gRNAs with PAM face inwards towards each other, please set paired.orientation = "PAMin".

To obtain the most recent dev version of CRISPRseek, please type the following command in a terminal. git clone git@git.bioconductor.org:packages/CRISPRseek Alternatively, you can type the following commands in a R/Rstudio session. BiocManager::install(version='devel') BiocManager::install("CRISPRseek")

Before installing it using the above R commands, please check the version at http://bioconductor.org/packages/devel/bioc/html/CRISPRseek.html to make sure the newest version has been propagated.

Best regards, Julie

ADD COMMENTlink modified 4 months ago • written 4 months ago by Julie Zhu4.0k

Thank you so much Dr. Zhu! I will give this a try.

ADD REPLYlink written 4 months ago by saba.parvez0
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