Questions tagged [crispr]

For questions about the CRISPER-Cas9 genome editing technology

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10 votes
1 answer
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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,...
Sarah Carl's user avatar
8 votes
2 answers
567 views

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 ...
natasa's user avatar
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5 votes
1 answer
111 views

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 ...
Cody Glickman's user avatar
3 votes
1 answer
60 views

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 ...
Cassie Bishop's user avatar
2 votes
3 answers
405 views

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 ...
gringer's user avatar
  • 13k
2 votes
1 answer
253 views

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 ...
Ina's user avatar
  • 21
2 votes
0 answers
94 views

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: ...
0x90's user avatar
  • 1,417
1 vote
1 answer
293 views

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 ...
codexero's user avatar
1 vote
1 answer
618 views

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 ...
Swimming bird's user avatar
1 vote
0 answers
18 views

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 ...
Research HMBR's user avatar
1 vote
0 answers
46 views

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 ...
geom_na's user avatar
  • 219
0 votes
1 answer
28 views

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 ...
user16558's user avatar
0 votes
2 answers
89 views

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 ...
0x90's user avatar
  • 1,417