sgRNA design for Campylobacter genome

[StephenLi55]

Hi,

I am trying to design sgRNA for campylobacter, but realised the campylobacter genome sequence is not available in the shiny app. Is there a way to upload my own genome sequence into the app?

best wishes,

Stephen

[dylanbeeber]

Hi Stephen,

It appears that there is no campylobacter genome available through BSgenome, so you would have to upload upload your own. To do this, I would first obtain fasta files containing the campylobacter genome and follow the instructions here for forging a BSgenome package. Once the BSgenome has been forged, you should be able to use the genome with the function sgRNA_design().

Right now there is no way to add a genome to the app without changing the app code. However if you were so inclined this could be done by adding something along the lines of: "campylobacter" = "name.of.your.forged.genome", to the "genome_select" input in the RunShiny.R script.

Best,
Dylan

[narsi05]

Hi,

I am trying to design gRNAs to target human gene sequences. I was able to upload the human genome gtf. After clicking on find gRNAs after some time the window of gRNA design tool is disappearing. In browser, it is becoming inactive.

Warning: Error in +: non-numeric argument to binary operator
2: shiny::runApp
1: crispRdesignRUI

Can you help in solving the problem?

[dylanbeeber]

Hi narsi05,

Thank you for bringing this to my attention. I believe I determined the cause of the "non-numeric argument" issue and it should now be working as expected in both the app and command line version. The fixes have been pushed to github but it may take a few days to push to cran. Let me know if you are experiencing any other issues.