[BioC] CRISPRseek question on scoring

Andy Crouse andy at transomic.com
Wed Aug 13 17:09:43 CEST 2014

Re: CRISPRseek question on scoring

Thank you Julie!

So, if I understand correctly, then if there were to be a
“top100offtargetTotalScore” column in the CRISPRseek summary file and the
score there was 10, then the crispr.mit.edu site would return a score of 90?

And I can expect that (100 – [CRISPRseek top5OfftargetTotalScore ]) to be
greater than the score from the MIT site?

Thank you again!  This is very helpful and I really like the flexibility of
the module.


*From:* Zhu, Lihua (Julie) [mailto:Julie.Zhu at umassmed.edu]
*Sent:* Wednesday, August 13, 2014 9:16 AM
*To:* Andy Crouse
*Cc:* bioconductor at r-project.org
*Subject:* Re: CRISPRseek question on scoring


Thanks for the feedback!

I assume you are comparing the scores in the summary file not the
individual offtarget output file. The score for each individual offtarget
should be the same between these two. However the summary score of
CRISPRseek has difference meaning from that of the web application. As a
summary, CRISPRseek adds the topN per user’s choice  of
topN.OfftargetTotalScore, eg., 5 or 10 off target scores together,
reasoning that the top off-targets are the most critical ones. The CRISPR
design website ranks guides based on an aggregate score using the top 100
matches (details at *http://crispr.mit.edu/about
<http://crispr.mit.edu/about>* - under "aggregate scores").  It is
important to note that their scale goes in the opposite direction, where
scores start at 100% and subtract the weighted off target score, whereas
our summary score starts at zero and adds the individual score of each off

Hope that is clear.  Please let me know if you need additional information.



On 8/13/14 1:57 AM, "Andy Crouse" <andy at transomic.com> wrote:

Hi Julie,
I am working with your CRISPRseek module.  I plugged in the example
sequence to the CRISPR.MIT.EDU <http://CRISPR.MIT.EDU>  site and it selects
the same gRNA, but the scores are very different.
The CRISPRseek guide says that the default uses the same weighting as Hsu
et al. The website scores are between 48 and 72 while the CRISPRseek scores
are between 5 and 20.  Am I interpreting something incorrectly or do I have
setting wrong?

This is what I ran:
offTargetAnalysis(inputFilePath, findgRNAsWithREcutOnly = FALSE,
REpatternFile = REpatternFile,findPairedgRNAOnly = FALSE,
BSgenomeName = Hsapiens,
txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
max.mismatch = 4, outputDir = outputDir, overwrite = TRUE)

Thanks for any assistance here.

Best Regards,


Andy Crouse, Ph.D.
Senior Product Manager
transOMIC Technologies

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