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
score there was 10, then the crispr.mit.edu site would return a score
And I can expect that (100 ? [CRISPRseek top5OfftargetTotalScore ]) to
greater than the score from the MIT site?
Thank you again! This is very helpful and I really like the
*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
should be the same between these two. However the summary score of
CRISPRseek has difference meaning from that of the web application. As
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
design website ranks guides based on an aggregate score using the top
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,
scores start at 100% and subtract the weighted off target score,
our summary score starts at zero and adds the individual score of each
Hope that is clear. Please let me know if you need additional
On 8/13/14 1:57 AM, "Andy Crouse" <andy at="" transomic.com=""> wrote:
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
the same gRNA, but the scores are very different.
The CRISPRseek guide says that the default uses the same weighting as
et al. The website scores are between 48 and 72 while the CRISPRseek
are between 5 and 20. Am I interpreting something incorrectly or do I
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.
Andy Crouse, Ph.D.
Senior Product Manager
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