README.md

In zhezhangsh/Rnaseq:

Rnaseq

An R package for tasks related to RNA-seq data

To load library within your R console

library(devtools);
install_github("zhezhangsh/Rnaseq");
library(Rnaseq);

Align reads with STAR

• Under unix/linux shell, copy these 2 files into your working directory, preferentially where the outputs will be

wget https://raw.githubusercontent.com/zhezhangsh/Rnaseq/master/examples/RunStar.yaml
wget https://raw.githubusercontent.com/zhezhangsh/Rnaseq/master/examples/RunStar.r

• Edit the RunStar.yaml file to specify inputs. Refer to STAR manual for details: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf
• Create the shell command by running the R script and run the script. (Make sure R is installed and Rscript is in your PATH)

Rscript ./RunStar.r ./RunStar.yaml ./RunStar.sh
nohup sh ./RunStar.sh

zhezhangsh/Rnaseq documentation built on May 4, 2019, 11:20 p.m.