CRISPinatoR_database
This repository contains database generating source codes for CRISPinatoR
This source codes includes following functions:
- Load Ensembl data including gene, transcript, and exon annotation.
- Search sgRNA candidates from exonic regions defined by Ensembl data.
- Annotate distance from the sgRNA candidates to closest ESE (Exon Splicing Enhancer).
- Off-target search for the sgRNA candidates.
- Write the sgRNA candidates into a tab-delimetered text file.
To generate the database, below data is required. Example data can be downloaded here.
- Ensembl data downloaded from here (Preprocessing is required). A whole data file for hg19 can be downloaded here.
- Reference FASTA file. It should be indexed by bwa and samtools faidx command.
- List of known ESE as a plain text file. For each line, the first tab-delimetered word will be regarded as an ESE.
To test this source codes, please follow instructions below.
- clone this repository.
git clone https://github.com/hwanglab/CRISPinatoR_database.git
- Download the example data above, then extract the zip file to a directory.
wget https://drive.google.com/open?id=1_o31dnXGel2W-SdCw-XW3DtBaZdCJdVJ
unzip example_data.zip
From 3 to 5, you can execute example.sh instead of type individual command.
- Compile source codes.
make
- Then index the reference file.
./CRISPinatoR index example_data/22.fa
samtools faidx example_data/22.fa
- Now you are ready to run the CRISPinatoR library construction. This command takes appoximately 1 hour to finish.
./CRISPinatoR library -r example_data/22.fa -d example_data/martquery_GRCh37_0819193157_65_tr_type_added.chr22.txt -e example_data/ese.txt -o hg19_sgRNA_list.txt