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Question: CRISPRseek scoring clarification
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gravatar for elspeth.ransom
8 months ago by
elspeth.ransom0 wrote:

I am working with the CRISPRseek R package and I am unsure on the meaning of the off target scores. 

Please could you clarify how the off-target score is calculated for the summary output (top 5 off target total score) and whether a higher or lower score is better (in terms of having lower chance of off-target effects).

Many Thanks!

ADD COMMENTlink modified 29 days ago by Julie Zhu3.8k • written 8 months ago by elspeth.ransom0
1
gravatar for Julie Zhu
29 days ago by
Julie Zhu3.8k
United States
Julie Zhu3.8k wrote:

Dawid,

FYI, I have updated the CRISPRseek package (Version: 1.17.5) to handle situations when the input gRNAs do not have any perfect match in the searching genome. I tested the package with your example code and gRNAs. Please let me know how it works out for you. Thanks for the feedback!

Best regards,

Julie

ADD COMMENTlink written 29 days ago by Julie Zhu3.8k

Julie,

Thank you for your help. Is 1.17.5 version available as a devel version on Bioconductor? I can only see 1.17.3 (from 2017-09-05).

Thanks,
Dawid  

ADD REPLYlink written 29 days ago by Dawid G. Nowak0
1
Dawid, Please try to use the following command to download the most recent version. git clone git@git.bioconductor.org:packages/CRISPRseek Best regards, Julie From: "Dawid G. Nowak [bioc]" <noreply@bioconductor.org> Reply-To: "reply+0df74aaa+code@bioconductor.org" <reply+0df74aaa+code@bioconductor.org> Date: Thursday, October 19, 2017 at 4:39 PM To: "Zhu, Lihua (Julie)" <julie.zhu@umassmed.edu> Subject: [bioc] C: CRISPRseek scoring clarification Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User Dawid G. Nowak<https: support.bioconductor.org="" u="" 6790=""/> wrote Comment: CRISPRseek scoring clarification<https: support.bioconductor.org="" p="" 93049="" #101857="">: Julie, Thank you for your help. Is 1.17.5 version available as a devel version on Bioconductor? I can only see 1.17.3 (from 2017-09-05). Thanks, Dawid ________________________________ Post tags: crisprseek You may reply via email or visit C: CRISPRseek scoring clarification
ADD REPLYlink written 29 days ago by Julie Zhu3.8k

Hi Julie,

Thanks it works! 

I noticed that OffTarget file doesn't have columns: inExon, inIntron, entrez_id, gene. Is there any particular reason to skip them? Information coming from these columns is still interesting when you design non-targeting guide (negative/scramble control) to see if potential OffTargets are in exon, intron etc. What do you think?

Best regards,

Dawid

ADD REPLYlink written 29 days ago by Dawid G. Nowak0
1
Dawid, Glad that it works for you. If you set annotateExon = TRUE, txdb and orgAnn, then you should get the annotation information. I removed them for speeding up the test. BTW, I added your example as one of the integration tests in CRISPRseek. Hope it is all right with you. FYI, I changed the value for top1Hit.onTarget.MMdistance2PAM to “perfect match not found” in the summary output when there is no on-target found. I am running the integration tests. I will commit the changes later with version 1.17.6. Best, Julie Best, Julie From: "Dawid G. Nowak [bioc]" <noreply@bioconductor.org> Reply-To: "reply+e3e084e4+code@bioconductor.org" <reply+e3e084e4+code@bioconductor.org> Date: Thursday, October 19, 2017 at 9:54 PM To: "Zhu, Lihua (Julie)" <julie.zhu@umassmed.edu> Subject: [bioc] C: CRISPRseek scoring clarification Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User Dawid G. Nowak<https: support.bioconductor.org="" u="" 6790=""/> wrote Comment: CRISPRseek scoring clarification<https: support.bioconductor.org="" p="" 93049="" #101873="">: Hi Julie, Thanks it works! I noticed that OffTarget file doesn't have columns: inExon, inIntron, entrez_id, gene. Is there any particular reason to skip them? Information coming from these columns is still interesting when you design non-targeting guide (negative/scramble control) to see if potential OffTargets are in exon, intron etc. What do you think? Best regards, Dawid ________________________________ Post tags: crisprseek You may reply via email or visit C: CRISPRseek scoring clarification
ADD REPLYlink written 29 days ago by Julie Zhu3.8k

Thanks, I am glad my comments can help with the package!

Dawid

ADD REPLYlink written 29 days ago by Dawid G. Nowak0
0
gravatar for Julie Zhu
8 months ago by
Julie Zhu3.8k
United States
Julie Zhu3.8k wrote:
Elspeth, CRISPRseek adds the topN offtarget scores per user's choice of N (parameter topN.OfftargetTotalScore, default 10 )and outputs the topN.OfftargetTotalScore in the Summary.xls file, e.g., top10.OfftargetTotalScore or top50.OfftargetTotalScore. The rational is that the top off-targets are the most critical ones. The lower topN.OfftargetTotalScore is, the better. For detailed information on individual offtarget score, please look at the OfftargetAnalysis.xls file. BTW, if you are working on spCas9 (gRNA length 20 and PAM = "NGG"), then you can set scoring.method = "CFDscore" to use an improved off target scoring algorithm which ranges from 0 to 1 instead of 0-100 for the Hsu-Zhang method. For detailed parameter setting and references, please type help(offTargetAnalysis) in a R session. Best, Julie From: "elspeth.ransom [bioc]" <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> Reply-To: "reply+8cb73ff9+code@bioconductor.org<mailto:reply+8cb73ff9+code@bioconductor.org>" <reply+8cb73ff9+code@bioconductor.org<mailto:reply+8cb73ff9+code@bioconductor.org>> Date: Friday, February 24, 2017 12:32 PM To: Lihua Julie Zhu <julie.zhu@umassmed.edu<mailto:julie.zhu@umassmed.edu>> Subject: [bioc] CRISPRseek scoring clarification Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User elspeth.ransom<https: support.bioconductor.org="" u="" 12442=""/> wrote Question: CRISPRseek scoring clarification<https: support.bioconductor.org="" p="" 93049=""/>: I am working with the CRISPRseek R package and I am unsure on the meaning of the off target scores. Please could you clarify how the off-target score is calculated for the summary output (top 5 off target total score) and whether a higher or lower score is better (in terms of having lower chance of off-target effects). Many Thanks! ________________________________ Post tags: crisprseek You may reply via email or visit CRISPRseek scoring clarification
ADD COMMENTlink written 8 months ago by Julie Zhu3.8k
Elspeth, This post might be helpful to you CRISPRseek question on scoring Best, Julie From: "Julie Zhu [bioc]" <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> Reply-To: "reply+b0d33c38+code@bioconductor.org<mailto:reply+b0d33c38+code@bioconductor.org>" <reply+b0d33c38+code@bioconductor.org<mailto:reply+b0d33c38+code@bioconductor.org>> Date: Friday, February 24, 2017 1:00 PM To: Lihua Julie Zhu <julie.zhu@umassmed.edu<mailto:julie.zhu@umassmed.edu>> Subject: [bioc] A: CRISPRseek scoring clarification Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User Julie Zhu<https: support.bioconductor.org="" u="" 3596=""/> wrote Answer: CRISPRseek scoring clarification<https: support.bioconductor.org="" p="" 93049="" #93052="">: Elspeth, CRISPRseek adds the topN offtarget scores per user's choice of N (parameter topN.OfftargetTotalScore, default 10 )and outputs the topN.OfftargetTotalScore in the Summary.xls file, e.g., top10.OfftargetTotalScore or top50.OfftargetTotalScore. The rational is that the top off-targets are the most critical ones. The lower topN.OfftargetTotalScore is, the better. For detailed information on individual offtarget score, please look at the OfftargetAnalysis.xls file. BTW, if you are working on spCas9 (gRNA length 20 and PAM = "NGG"), then you can set scoring.method = "CFDscore" to use an improved off target scoring algorithm which ranges from 0 to 1 instead of 0-100 for the Hsu-Zhang method. For detailed parameter setting and references, please type help(offTargetAnalysis) in a R session. Best, Julie From: "elspeth.ransom [bioc]" <noreply@bioconductor.org<mailto:noreply@bioconductor.org><mailto:noreply@bioconductor.org>> Reply-To: "reply+8cb73ff9+code@bioconductor.org<mailto:reply+8cb73ff9+code@bioconductor.org><mailto:reply+8cb73ff9+code@bioconductor.org>" <reply+8cb73ff9+code@bioconductor.org<mailto:reply+8cb73ff9+code@bioconductor.org><mailto:reply+8cb73ff9+code@bioconductor.org>> Date: Friday, February 24, 2017 12:32 PM To: Lihua Julie Zhu <julie.zhu@umassmed.edu<mailto:julie.zhu@umassmed.edu><mailto:julie.zhu@umassmed.edu>> Subject: [bioc] CRISPRseek scoring clarification Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User elspeth.ransom<https: support.bioconductor.org="" u="" 12442=""/> wrote Question: CRISPRseek scoring clarification<https: support.bioconductor.org="" p="" 93049=""/>: I am working with the CRISPRseek R package and I am unsure on the meaning of the off target scores. Please could you clarify how the off-target score is calculated for the summary output (top 5 off target total score) and whether a higher or lower score is better (in terms of having lower chance of off-target effects). Many Thanks! ________________________________ Post tags: crisprseek You may reply via email or visit CRISPRseek scoring clarification<https: support.bioconductor.org="" p="" 93049=""/> ________________________________ Post tags: crisprseek You may reply via email or visit A: CRISPRseek scoring clarification
ADD REPLYlink written 8 months ago by Julie Zhu3.8k

Hi Julie,

I have a question about "CFDscore". My understanding is that top50.OfftargetTotalScore is calculated by adding adding topN scores together.

I can see my top50.OfftargetTotalScore/top100.OfftargetTotalScore is NA (which I assume no offTargets?). When I look for offTarget at guide with the top10 score NA I can see a a "CFD score" calculated for only one site and I see a number i.e. 0.2. I would assume that top10 would be still calculated but would only contain 0.2 even if there are no other values?

### my code below, I test a set of mine guides

offTargetAnalysis(inputFilePath,

                  REpatternFile = REpatternFile,
                  scoring.method = "CFDscore",
                  format = "fasta",
                  findgRNAs = FALSE, # important for testing to set FALSE
                  findgRNAsWithREcutOnly = FALSE, # if FALSE not restr. enzymes
                  findPairedgRNAOnly = FALSE,
                  gRNA.name.prefix = "sg.",                 
                  orgAnn = orgAnn,
                  BSgenomeName = BSgenomeName,
                  txdb = txdb,
                  chromToSearch= "all", # change here for all to look at all chromosomes
                  min.gap = 0, max.gap = 20,
                  max.mismatch = 3,
                  min.score = 0.1, 
                  topN = 100,
                  topN.OfftargetTotalScore= 10, # 10 top Offtarget will be calculated 
                  annotateExon = TRUE,
                  fetchSequence = TRUE, upstream = 250, downstream = 250,
                  overlap.gRNA.positions = c(17, 18), 
                  PAM.size = 3,
                  PAM = "NGG",
                  gRNA.size = 20, 
                  outputDir = outputDir,
                  overwrite = TRUE)

 

ADD REPLYlink written 4 weeks ago by Dawid G. Nowak0
Hi Dawid, Is this a unique problem with scoring.method = "CFDscore"? Thanks! Best regards, Julie From: "Dawid G. Nowak [bioc]" <noreply@bioconductor.org> Reply-To: "reply+c0630670+code@bioconductor.org" <reply+c0630670+code@bioconductor.org> Date: Tuesday, October 17, 2017 at 1:36 PM To: "Zhu, Lihua (Julie)" <julie.zhu@umassmed.edu> Subject: [bioc] C: CRISPRseek scoring clarification Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User Dawid G. Nowak<https: support.bioconductor.org="" u="" 6790=""/> wrote Comment: CRISPRseek scoring clarification<https: support.bioconductor.org="" p="" 93049="" #101727="">: Hi Julie, I have a question about "CFDscore". My understanding is that top50.OfftargetTotalScore is calculated by adding adding topN scores together. I can see my top50.OfftargetTotalScore/top100.OfftargetTotalScore is NA (which I assume no offTargets?). When I look for offTarget at guide with the top10 score NA I can see a a "CFD score" calculated for only one site and I see a number i.e. 0.2. I would assume that top10 would be still calculated but would only contain 0.2 even if there are no other values? ### my code below, I test a set of mine guides offTargetAnalysis(inputFilePath, REpatternFile = REpatternFile, scoring.method = "CFDscore", format = "fasta", findgRNAs = FALSE, # important for testing to set FALSE findgRNAsWithREcutOnly = FALSE, # if FALSE not restr. enzymes findPairedgRNAOnly = FALSE, gRNA.name.prefix = "sg.", orgAnn = orgAnn, BSgenomeName = BSgenomeName, txdb = txdb, chromToSearch= "all", # change here for all to look at all chromosomes min.gap = 0, max.gap = 20, max.mismatch = 3, min.score = 0.1, topN = 100, topN.OfftargetTotalScore= 10, # 10 top Offtarget will be calculated annotateExon = TRUE, fetchSequence = TRUE, upstream = 250, downstream = 250, overlap.gRNA.positions = c(17, 18), PAM.size = 3, PAM = "NGG", gRNA.size = 20, outputDir = outputDir, overwrite = TRUE) ________________________________ Post tags: crisprseek You may reply via email or visit C: CRISPRseek scoring clarification
ADD REPLYlink written 4 weeks ago by Julie Zhu3.8k

Hi,

I just tested both scoring methods and I see this situation with NA in both cases. I made some comments below, I started to notice them when I test target and off-target analysis for my specified gRNAs. I use CRISPRseek 1.16.0

1) When I assign x <-  offTargetAnalysis(), then I can see x$summary but I cannot see anything in Summary.xls created by the package.

2) I  also noticed a discrepancy between TopN score calculated in Summary and OfftargetAnalysis.,  i.e. if I take top5 hits from OfftargetAnalysis and sum up I see a different number than in Summary.

Thanks,

Dawid

 

# below example of guide that gave me NA scores but scores where still calculated 

>sg.test2

GACCGGAACGATCTCGCGTANGG

ADD REPLYlink written 4 weeks ago by Dawid G. Nowak0
Dawid, Thanks for testing both scoring methods! It might be an issue with data type. Could you please send me the testing input file, the code and the output?My email is Julie.zhu@umassmed.edu<mailto:julie.zhu@umassmed.edu>. Thanks! Best regards, Julie From: "Dawid G. Nowak [bioc]" <noreply@bioconductor.org> Reply-To: "reply+0ad43044+code@bioconductor.org" <reply+0ad43044+code@bioconductor.org> Date: Tuesday, October 17, 2017 at 4:46 PM To: "Zhu, Lihua (Julie)" <julie.zhu@umassmed.edu> Subject: [bioc] C: CRISPRseek scoring clarification Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User Dawid G. Nowak<https: support.bioconductor.org="" u="" 6790=""/> wrote Comment: CRISPRseek scoring clarification<https: support.bioconductor.org="" p="" 93049="" #101731="">: Hi, I just tested both scoring methods and I see this situation with NA in both cases. I made some comments below, I started to notice them when I test target and off-target analysis for my specified gRNAs. I use CRISPRseek 1.16.0 1) When I assign x <- offTargetAnalysis(), then I can see x$summary but I cannot see anything in Summary.xls created by the package. 2) I also noticed a discrepancy between TopN score calculated in Summary and OfftargetAnalysis., i.e. if I take top5 hits from OfftargetAnalysis and sum up I see a different number than in Summary. Thanks, Dawid # below example of guide that gave me NA scores but scores where still calculated >sg.test2 GACCGGAACGATCTCGCGTANGG ________________________________ Post tags: crisprseek You may reply via email or visit C: CRISPRseek scoring clarification
ADD REPLYlink written 4 weeks ago by Julie Zhu3.8k
1
Dawid, Thanks for the test script and input! When there is no on-target found for any input gRNAs, summary.xls file will be empty. Also, the topN score is calculated assuming the on-target is present for the gRNA (sum(2nd, Nth)) I am updating the dev code to handle this exception and will post an update in the support site. Thanks again for reporting the issue! Best, Julie Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User Julie Zhu<https: support.bioconductor.org="" u="" 3596=""/> wrote Comment: CRISPRseek scoring clarification<https: support.bioconductor.org="" p="" 93049="" #101740="">: Dawid, Thanks for testing both scoring methods! It might be an issue with data type. Could you please send me the testing input file, the code and the output?My email is Julie.zhu@umassmed.edu<mailto:julie.zhu@umassmed.edu>. Thanks! Best regards, Julie From: "Dawid G. Nowak [bioc]" <noreply@bioconductor.org> Reply-To: "reply+0ad43044+code@bioconductor.org" <reply+0ad43044+code@bioconductor.org> Date: Tuesday, October 17, 2017 at 4:46 PM To: "Zhu, Lihua (Julie)" <julie.zhu@umassmed.edu> Subject: [bioc] C: CRISPRseek scoring clarification Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User Dawid G. Nowak<https: support.bioconductor.org="" u="" 6790=""/> wrote Comment: CRISPRseek scoring clarification<https: support.bioconductor.org="" p="" 93049="" #101731="">: Hi, I just tested both scoring methods and I see this situation with NA in both cases. I made some comments below, I started to notice them when I test target and off-target analysis for my specified gRNAs. I use CRISPRseek 1.16.0 1) When I assign x <- offTargetAnalysis(), then I can see x$summary but I cannot see anything in Summary.xls created by the package. 2) I also noticed a discrepancy between TopN score calculated in Summary and OfftargetAnalysis., i.e. if I take top5 hits from OfftargetAnalysis and sum up I see a different number than in Summary. Thanks, Dawid # below example of guide that gave me NA scores but scores where still calculated >sg.test2 GACCGGAACGATCTCGCGTANGG ________________________________ Post tags: crisprseek You may reply via email or visit C: CRISPRseek scoring clarification<https: support.bioconductor.org="" p="" 93049="" #101731=""> ________________________________ Post tags: crisprseek You may reply via email or visit C: CRISPRseek scoring clarification
ADD REPLYlink written 4 weeks ago by Julie Zhu3.8k
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