Question

How to understand Summary.xls in output of CRISPRseek

1

Entering edit mode

Ou, Jianhong ★ 1.3k

@ou-jianhong-4539

Last seen 19 hours ago

United States

Hi Julie,

I want to double check that I correctly understand each column of summary.xls in output of CRISPRseek. Thank you.

names : name of gRNA

forViewInUCSC : coordinates

extendedSequence : extended sequence of gRNA

gRNAefficacy : gRNA efficacy. The higher the better. see [https://www.nature.com/articles/nbt.3026](Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation)

gRNAsPlusPAM : sequence of gRNAs plus PAM

top5OfftargetTotalScore : total score of top 5 offtarget. The higher the possibility to get off targets.

top10OfftargetTotalScore : total score of top 10 offtarget

top1Hit.onTarget.MMdistance2PAM : mismatch distance to PAM of the top 1 hit on target

topOfftarget`N`MMdistance2PAM : mismatch distance to PAM of the top N hit off target

REname : restriction enzyme name

uniqREin200 : unique restriction enzyme name in upstream 200 and downstream 200 from gRNA.

Jianhong

crisprseek • 1.1k views

ADD COMMENT • link updated 6.5 years ago by Julie Zhu ★ 4.3k • written 6.5 years ago by Ou, Jianhong ★ 1.3k

score 0 · Answer 1 · 2018-06-08

0

Entering edit mode

Julie Zhu ★ 4.3k

@julie-zhu-3596

Last seen 12 months ago

United States

Jianhong, Your understanding of all the columns is correct except uniqueREin200, which contains the unique restriction enzyme names in upstream 100 and downstream 100 around the gRNA. Best, Julie

ADD COMMENT • link 6.5 years ago Julie Zhu ★ 4.3k

0

Entering edit mode

Thank you Julie for the correction. Jianhong. From: "Julie Zhu [bioc]" <noreply@bioconductor.org> Reply-To: "reply+e0a20045+code@bioconductor.org" <reply+e0a20045+code@bioconductor.org> Date: Friday, June 8, 2018 at 10:05 AM To: "Jianhong Ou, Ph.D." <jianhong.ou@duke.edu> Subject: [bioc] A: How to understand Summary.xls in output of CRISPRseek Activity on a post you are following on support.bioconductor.org<https: urldefense.proofpoint.com="" v2="" url?u="<a href=" http:="" <a="" href="http://https-3A__support.bioconductor.org" rel="nofollow">https-3A__support.bioconductor.org"="" rel="nofollow">https-3A__support.bioconductor.org&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=ljB-qWl6rA7xw2MEOhKxF7VZfRhcDX3SvAiZPEMkfIw&s=t8cN0zhzEhd22Zr0DdErzY-2T1JwSrJS5sJOgejTjPU&e="> User Julie Zhu<https: urldefense.proofpoint.com="" v2="" url?u="https-3A__support.bioconductor.org_u_3596_&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=ljB-qWl6rA7xw2MEOhKxF7VZfRhcDX3SvAiZPEMkfIw&s=hUQNDkRqviwZT_y3eREVhR4ZY-NoJgicTbrY8SAt_r0&e="> wrote Answer: How to understand Summary.xls in output of CRISPRseek<https: urldefense.proofpoint.com="" v2="" url?u="https-3A__support.bioconductor.org_p_109830_-23109831&d=DwMCaQ&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=PXg851DHXyo-Gs3eMIfeo49gUXVh-JSZu_MZDDxGun8&m=ljB-qWl6rA7xw2MEOhKxF7VZfRhcDX3SvAiZPEMkfIw&s=xBX5zfe9P6Pzw42PGzv_UevwbLdaQ9kKT3EgVRslY8s&e=">: Jianhong, Your understanding of all the columns is correct except uniqueREin200, which contains the unique restriction enzyme names in upstream 100 and downstream 100 around the gRNA. Best, Julie ________________________________ Post tags: crisprseek You may reply via email or visit A: How to understand Summary.xls in output of CRISPRseek

ADD REPLY • link 6.5 years ago Ou, Jianhong ★ 1.3k