News: CRISPRseek: generate gRNAs in bed format, useScore argument
gravatar for Julie Zhu
3.1 years ago by
Julie Zhu3.8k
United States
Julie Zhu3.8k wrote:


Per your suggestion, the new release produces bed formatted gRNAs. By default, the gRNAs will be displayed with gray scale to reflect the gRNA efficacy [1]. The darker the higher efficacy. You can change it to colored plot by setting UseScore = FALSE in offTargetAnalysis.
UseScore: Default TRUE, display in gray scale with the darkness indicating the gRNA efficacy. The taller bar shows the Cas9 cutting site. If set to False, efficacy will not show. Instead, gRNAs in plus strand will be colored red and gRNAs in negative strand will be colored green.

1. Doench JG, Hartenian E, Graham DB, Tothova Z, Hegde M, Smith I, Sullender M, Ebert BL, Xavier RJ, Root DE. Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nat Biotechnol. 2014 Sep 3. doi: 10.1038 nbt.3026

Thanks for your input!

Best regards,


On 10/8/14 4:47 PM, "Ilbay, Orkan" <> wrote:

Dear Dr. Zhu,

Thank you for the talk today and for the CRISPRseek package.

I used CRISPRseek to identify gRNA candidates which would help me introduce cuts at certain points in the C.elegans genome. These point should be close (closer the better) to the regions where I am planing to change by HR. So, one thing people like me would find useful is to be able to visualize the candidate gRNAs on the UCSC genome browser. That could be very easy to do if CRISPRseek had an output format like .gff3 or .bed.

I have attached a .bed file (which can be added as a track file to the genome browser) and a PNG picture that shows how this track looks on the genome browser. This .bed file also has the locations that I want to mutate which allows me to see where the candidate gRNAs are located with respect to the target sites.

I hope you find my experience useful. And, I would really love to see alternative output formats or other means of visualizing the CRISPRseek results.

Thakn you so much,


Orkan Ilbay,
PhD Candiate,
Ambros Lab.

ADD COMMENTlink modified 3.1 years ago by orkanilbay0 • written 3.1 years ago by Julie Zhu3.8k
gravatar for orkanilbay
3.1 years ago by
United States
orkanilbay0 wrote:

Works great! Thank you, Dr. Zhu!

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by orkanilbay0
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