Commit 2de2297c authored by harm's avatar harm
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Delete Readme.txt

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################################################################################
### README #####################################################################
If you are using our software, please cite:
Hans-Hermann Wessels, Alejandro Méndez-Mancilla, Xinyi Guo, Mateusz Legut, Zharko Daniloski, Neville E. Sanjana.
Principles for rational Cas13d guide design. bioRxiv (2019). doi:10.1101/2019.12.27.889089
This R-script software serves to predict guides for RfxCas13d Type-IV CRISPR proteins to maximize knock-down efficiencies.
Guide efficacies are modeled after an on-target tilling screen against GFP, CD46, CD55, and CD71 mRNA.
# Installation
You have already unpacked Cas13design.tar.gz
tar -xzf Cas13design.tar.gz
Unpacking Cas13design.tar.gz will create a Cas13design directory, as well as scripts and data sub-directories.
The main executable RfxCas13d_GuideScoring.R can be found within the scripts sub-directory.
External RNAfold and RNAplfold binaries v2.4.10 are included. RNAhybrid may be installed and added to your $PATH (see below).
All R packages needed will be automatically installed within the scripts folder upon the first execution.
This may increase the runtime of the first run by several minutes. We recommend using R v3.6 or newer to execute RfxCas13d_GuideScoring.R.
If older R versions are used, the Bioconductor package Biostrings may need to be installed manually via BiocLite.
Model input data as well as an example input fasta file are included within the data sub-sirectory.
Next, please install RNAhybrid.
The source code can be downloaded here:
wget https://bibiserv.cebitec.uni-bielefeld.de/applications/rnahybrid/resources/downloads/RNAhybrid-2.1.2.tar.gz
copy RNAhybrid-2.1.2.tar.gz into ./Cas13design/scripts/ and unpack RNAhybrid
cp RNAhybrid-2.1.2.tar.gz ./Cas13design/scripts/
cd ./Cas13design/scripts/
tar -xzf RNAhybrid-2.1.2.tar.gz
cd RNAhybrid-2.1.2
Follow the installation instructions for RNAhybrid in INSTALL:
If you install it on your local system and you have sudo rights, do:
./configure
make
make install
If you install it e.g. on a cluster without sudo rights you can follow this:
./configure --prefix=$HOME #this will create a bin folder in your $HOME directory
make
make install
export PATH=$HOME/bin:$PATH # You may want to add this to your ~/.bashrc or ~/.bash_profile
Make sure RNAhybrid has been added to your PATH
which RNAhybrid # should return ~/bin/RNAhybrid
The Software will assume RNAhybrid is in ~/bin/
All other dependencies are included in the Cas13design.tar.gz archive
# Predict guides
To predict guide RNA efficacies simply call RfxCas13d_GuideScoring.R with its three required input arguments in order. In its current implmentation, the script will run successfully only within its main directory Cas13design.
cd Cas13design
Rscript <script.R> <input fasta> <model input> <plot logical>
The input fasta file should contain a single entry.
Running multiple prediction is faster, if separate instances are coerced.
The fasta header contains its name. Additional information is expected to be separated by "|". CDS coordinates, if present, should be provided in the following format within the fasta header (e.g. CDS:171-2453). These coordinates only become relevant, if you desire to plot guide predictions along cds-containing transcripts.
Run the example data:
Rscript ./scripts/RfxCas13d_GuideScoring.R ./data/test.fa ./data/Cas13designGuidePredictorInput.csv true
If you run the script the first time, R package installation may take several minutes.
Once Cas13design is fully installed, the run time scales with the fasta input length.
The minimum length supplied must be at least 30 nucleotides. The total run time for the provided ~1000nt test.fa example is about 2 min and 10 sec.
# Expected outputs
The output may be 3-fold and named after the fasta header information:
1) A fasta file with guide sequences (reverse complement to the target sequence).
The header includes the following information separated by underscores "_"
the crRNA number (5' to 3') and match position (e.g. crRNA1156:1399-1425)
standardized guide score
rank
quartile according to input screens
2) A csv file containing all predicted guides
3) if plot was set to TRUE, a pdf file is returned depicting the score destribution along the target transcripts
Guide scores range between a 0 - 1 interval, with higher scores being indicative for higher predicted knock-down efficacy.
# Additional information
For more information, please refer to our manuscript.
################################################################# /README ######
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################################################################################
### COPYRIGHT ##################################################################
# New York Genome Center
# Copyright (c) 2019 Hans-Hermann Wessels and Neville Sanjana.
# Released under BSD 3. See LICENSE file for details.
# If you're interested in getting access to this system under a different license, please contact us.
# Version: 0.2
# Author: Hans-Hermann Wessels
################################################################# /COPYRIGHT ###
################################################################################
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