User: joyce

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joyce0
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Posts by joyce

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Comment: C: CRISPRseek offTargetAnalysis errors
... Hi Julie, Thanks for looking into this issue for me. Before I received your response to my question, I edited the post and added another question (B) on a different error message. You might not have seen it. I copied it below: (B) *Building feature vectors for scoring ...* *Calculating scores ...
written 8 months ago by joyce0
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Comment: C: CRISPRseek offTargetAnalysis errors
... Hi Julie, Here are two DNA sequences that incur the error: seq1: ATGGCTTCACAGCTGCCTTTTCCTGCAGACGACTTCGGTATCTACTATGTCCT seq2: ATGGCGGATATGGAGGACCTTTTCGGGAGCGACGTCGACAGTGATGCTGAGCGTAAAG Thanks for your help! Joyce Joyce On Fri, Jan 12, 2018 at 11:07 AM, Julie Zhu [bioc] <noreply@bioconduct ...
written 8 months ago by joyce0
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CRISPRseek offTargetAnalysis errors
... Hi Julie, We have been running offTargetAnalysis on a large set of sequences.  For some of the sequences, we ran into the following 2 kinds of error messages: (A) Searching for gRNAs ... Error in .Call2("new_XStringSet_from_CHARACTER", ans_class, ans_elementType, : key 69 (char 'E') not in looku ...
crisprseek written 8 months ago by joyce0
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CRISPRseek offTargetAnalysis error
... Hi Julie, I am running offTargetAnalysis to find gRNAs and their off-targets in some sequences. For a couple of sequences, I got the following error message while the program was trying to find all hits in a particular sequence: "Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed ...
crisprseek written 9 months ago by joyce0 • updated 9 months ago by Julie Zhu3.8k
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CRISPRseek gRNA efficacy
... Hi Julie, I noticed an option, "useEfficacyFromInputSeq", in offTargetAnalysis.  Could you please explain how the gRNA efficacy is calculated from off-target analysis, and how is it different from the one calculated from the input sequence?  Does either correspond to the Rule Set 2 scoring methods ...
crisprseek written 10 months ago by joyce0 • updated 10 months ago by Julie Zhu3.8k
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Comment: C: CRISPRseek CFD score
... Thank you, Julie.  I found out the source of our problem - in our GFF file, the chromosome names were not in the form of chr1, chr2, ... etc.  After making the proper modifications, I was able to get the exon annotations. Thanks again for your help! Joyce ...
written 11 months ago by joyce0
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Comment: C: CRISPRseek CFD score
... Hi Julie, I don't find the exon annotation in the OfftargetAnalysis.xls file.  I list the information you requested below: (1) > sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)   Matrix products: default BLAS/LAPACK: / ...
written 11 months ago by joyce0
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CRISPRseek CFD score
... Hi Julie, I am using offTargetAnalysis function with CFD scoring method (CRISPRseek verison 1.16.0 from bioconductor) to select a few best-scoring gRNAs for each of a large set of sequences.  In the past, I have used the combination of gRNAefficacy and top10OfftargetTotalScore in the summary file a ...
crisprseek written 11 months ago by joyce0 • updated 11 months ago by Julie Zhu3.8k
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could not find function "hash"
... Hi Julie, I am using offTargetAnalysis to find gRNAs with CFDscores. I followed the manual and included the subPAM.activity option as follows: results=offTargetAnalysis("exon.fasta", findgRNAsWithREcutOnly = FALSE, annotateExon = TRUE,findPairedgRNAOnly = FALSE, txdb= txdb, max.mismatch = 3, BSgen ...
crisprseek written 11 months ago by joyce0 • updated 11 months ago by Julie Zhu3.8k
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CFD scores for searchHits?
... I would like to find off-targets of the gRNAs we designed in a 30kb sequence. I could get the Hsu-Zhang scores with the combination of searchHits, buildFeatureVectorForScoring, and getOfftargetScore.  Is it possible to get the CFD scores with some options?   Thank you! ...
crisprseek written 11 months ago by joyce0 • updated 11 months ago by Julie Zhu3.8k

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