Questions tagged [crispr]
For questions about the CRISPER-Cas9 genome editing technology
13
questions
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CRISPR genome wide screen analysis using MAGeCK-- Loss of reads/sgRNA using MAGeCK count function?
Sorry if this question seems basic. I am trying to run the MAGeCK pipeline to analyze CRISPR knockout screen data produced by someone in my lab around 5 years ago. I was given the data as bam files ...
0
votes
1
answer
28
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Keep first 20 nucleotides of sequences using R
I have an Excel sheet from the CRISPR library where I have sequences of gRNAs (with 30 nucleotides) in a column and I only need to keep the first 20 nucleotides for those gRNAs and delete the rest ...
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vote
0
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Which components must be included in the HDR plasmid?
I am trying to design a plasmid for our knock in experiment and wanted to clarify some technical issues.
I wanted to know exactly which components must be included in the plasmid.
I know that I have ...
1
vote
1
answer
293
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Find CRISPR PAM-sites with python
I am a college student and just started bioinformatics. I am trying to write a script (not for school) that finds all potential NGG and TTTN protospacer adjacent motif sequences in a genome string. I ...
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CRISPR Screen Control - What genes do not affect phenotype when knocked out?
I have some raw read count data from a crispr screen.
The library used was addgene's
Mouse Improved Genome-wide Knockout CRISPR Library v2
I'm following an analysis pipeline that requires counts ...
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votes
2
answers
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CRISPR screening and systems biology
I am not sure how to tackle this one, so I’ll explain the general idea I have in mind.
Given results of a CRISPR knockout screening experiment (like in this paper) with two types of assays: control ...
- 1,417
1
vote
1
answer
618
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CRISPR/Cas9 screen analysis with Mageck: paired-end sequencing
I want to analyse data from a CRISPR/Cas9 screen (control vs. treatment) and I'm using Mageck (https://sourceforge.net/projects/mageck/). The problem is that I'm working with paired-end sequencing ...
2
votes
1
answer
253
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Read alignment using Bowtie2
So this is related to CRISPR-CAS9. I am working with off-target predictions for my thesis and was looking at all scientific papers related to CRISPR. I found one and decided to use their datasets. The ...
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2
votes
0
answers
94
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How to analyze and visualize CRISPR-CAS9 screening results?
I have a whole-gene CRISPR screening of an assay at different time points. I created a table of the gene number and the count of its reads:
...
- 1,417
5
votes
1
answer
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CRISPR Sequence Finder and Database Download
I am searching for tools to pull CRISPR Spacers from Bacterial Genomes. I am aware of the CRISPRDB and the corresponding identification tool on the web server.
Are there other tools for finding ...
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2
votes
3
answers
405
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How do I find the most similar sequences from a large set of short sequences?
I've been asked to evaluate whether the MinION will be sufficient to distinguish between 20bp CRISPR guide RNAs from the GeCKO v2 set. I know that this set has some exactly identical sequences, which ...
- 13k
8
votes
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R packages for data analyses of pooled CRISPR screens
We are designing a CRISPR/Cas9 experiment and thinking of the down-stream data analyses.
Are there any R packages for analysing raw NGS read count data from pooled genetic screens using CRIPSR/Cas9 ...
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10
votes
1
answer
144
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Large-scale gRNA design for a CRISPR screen
What are the best tools to design gRNAs in a high-throughput way for a CRISPR screen, e.g. targeting all protein-coding genes in a genome? I would like to take into account possible off-target effects,...
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