User: Dawid G. Nowak

Reputation:
10
Status:
New User
Location:
United States
Twitter:
@dawidgnowak
Last seen:
3 months, 2 weeks ago
Joined:
3 years, 12 months ago
Email:
d************@gmail.com

Posts by Dawid G. Nowak

<prev • 16 results • page 1 of 2 • next >
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CFDscore calculations used in CRISPRseek
... Hi, I have a question about “CFDscore" calculations used in CRISPRseek. I have a guide that I am testing against target DNA sequence using compare2Sequences(). I see some differences when I compare a table manually to the calculated score using compare2Sequences(). Just to be sure how “CFDscore" is ...
crisprseek cfdscore written 3 months ago by Dawid G. Nowak10 • updated 3 months ago by Julie Zhu3.8k
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Comment: C: CRISPRseek scoring clarification
... Thanks, I am glad my comments can help with the package! Dawid ...
written 11 months ago by Dawid G. Nowak10
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Comment: C: CRISPRseek scoring clarification
... 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 poten ...
written 11 months ago by Dawid G. Nowak10
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Comment: C: CRISPRseek scoring clarification
... 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   ...
written 11 months ago by Dawid G. Nowak10
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Comment: C: CRISPRseek scoring clarification
... 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 ...
written 11 months ago by Dawid G. Nowak10
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Comment: C: CRISPRseek scoring clarification
... 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 ...
written 11 months ago by Dawid G. Nowak10
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Comment: C: CRISPRseek with genome not available in BSgenome
... Thanks Julie, that works exactly as I needed. Dawid ...
written 14 months ago by Dawid G. Nowak10
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Comment: C: CRISPRseek with genome not available in BSgenome
... Julie, After updating to  format = c("fasta", "fasta") and changing some parameters I get: Error in offTargetAnalysisOfPeakRegions(gRNA = gRNAFile, peaks = fastaSequenceFile,  :    only bed file with at least 4 columns are supported Best, Dawid   ...
written 14 months ago by Dawid G. Nowak10
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Comment: C: CRISPRseek with genome not available in BSgenome
... Hi Julie, I am not sure if I understand this correctly. Can you test a guide(s) (in FASTA) on any type of sequence (not necessarily any genome sequence but i.e. "artificial" sequence of your interest)? I tried to run a code as you suggested above with guide and sequence of my interest (both in FAS ...
written 14 months ago by Dawid G. Nowak10
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offTargetAnalysis takes super long
... Hi, I am having recently problems with offTargetAnalysis() "Building feature vectors for scoring ... takes super long comparing to the previous runs and then I see this Error when I stop:   Error in unlist(lapply(1:dim(mismatch.pos)[1], function(i) { :    error in evaluating the argument 'x' in ...
crisprseek written 3.0 years ago by Dawid G. Nowak10 • updated 3.0 years ago by Julie Zhu3.8k

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