Skip to content

Latest commit

 

History

History
92 lines (53 loc) · 2.2 KB

README.md

File metadata and controls

92 lines (53 loc) · 2.2 KB
Raw

mm10db

This repository contains the whole-genome CRISPR target detection method as implemented in Sunagawa et al., "Mammalian Reverse Genetics without Crossing Reveals Nr3a as a Short-Sleeper Gene", Cell Reports 14(3.662-677, 2016)

Getting Started

Dependencies & Requirements

  • Python 2.7

  • FASTA formatted chromosome files (obtainable via UCSC.

    • Place these files in a new directory mm10_input/chr_sequences.

    • Concatenate all sequences into a single file named all_sequences.txt

    • Build Bowtie2 indexes for these

  • refGene annotation data (obtainable via UCSC)

    • Place this file in the mm10_input directory and name the file refGene.txt

Installing

  1. Clone this repository
git clone https://github.com/bmds-lab/mm10db.git
  1. Build the findMismatches_threads binary
cd <repo>
make pthread

Usage

  1. Prepare gene lists. This will generate file(s) in the mm10_input directory.
python prepareGeneListsWholeGenome.py
  1. Create list(s) of exons. Repeat for each list file generated in step 1.
python createListExons.py <listFile>

<listFile> is a file generated by createListExons.py. Use only the filename; strip the directory and file extension.

  1. Prepare the exon sequences files. Repeat for each list file generated in step 1.
python prepareExonSequences.py <listFile>

<listFile> is a file generated by createListExons.py. Use only the filename; strip the directory and file extension.

  1. Prepare list of off-target sites
python prepareListOfftargetSites.py
  1. Run method
python target_identitification_viaC.py nb_threads_C=<int> nb_threads_Bowtie=<int> genes=<listFile>

Note: we set nb_threads_C to 128 and nb_threads_Bowtie to 8

<listFile> is a file generated by createListExons.py. Use only the filename; strip the directory and file extension.

Citing

If you use this software, please cite the paper.

Sunagawa, G. A., Sumiyama, K., Ukai-Tadenuma, M., Perrin, D., Fujishima, H., Ukai, H., ... & Shimizu, Y. (2016). Mammalian reverse genetics without crossing reveals Nr3a as a short-sleeper gene. Cell reports, 14(3), 662-677.

License

See LICENSE