Repository for scripts associated with manuscript.
Associated paper: Roberson EDO. (2015) Identification of high-efficiency 3'GG gRNA motifs in indexed FASTA files with ngg2. PeerJ Computer Science 1:e33.
The top level directory contains the scripts necessary to repeat the analysis.
The figures directory contains the images generated during the final analysis using R Markdown.
- Linux + bash
- R, packages should prompt for install if needed
- make
- wget
- R Studio with knitr (to knit the RMd file)
- python, along with the ngg2 program
- the scripts from this repository
The makefile handles the entire analysis from file downloads to annoation of sites. There are several parameters you may wish to edit.
- species - this file contains a list of all species to download from Ensembl. Add or remove as you wish.
- num_ngg2_cpus - sets how many processors to run ngg2
- num_rscript_cpus - sets how many processors to run R analysis (may be memory intensive)
- ngg2_analysis.R - you may wish to change the registered parallel backend for R to use (make sure to deactivate at end of R script)
nohup make -f ngg2_datageneration.make 1>ngg2_paper.log 2>&1 &There are two versions of the data associated with this paper.
- Version 1
This was run with the early versions of ngg2 and ran a block scan. That means that if two gRNA sites overlap one another on the same strand, only the first is reported. Only 6 model species were tested.
- Version 2
This version was run with a more efficient, multiprocessing ngg2 version using exhaustive scanning to identify all 3'GG gRNA sites. Two additional species, African elephan and pigs, were added in this analysis.
| Data | Type | Preprint |
|---|---|---|
| Version 1 fileset | Block scan | ngg2 v1 |
| Version 2 fileset | Exhaustive scan |