README.md

In zhushijia/STAR2bSMRT: STARlong and STARshort based Single Molecule Real Time Iso-Seq analysis

STAR2bSMRT

STARlong and STARshort based Single Molecule Real Time Iso-Seq analysis

Description

STAR2bSMRT is a novel hybrid sequencing-based alternative splicing identification method, which is specially tailored for long read RNAseq correction. It was used in the paper (E Flaherty, S Zhu, et. al., Neuronal impact of patient-specific aberrant NRXN1α splicing, Nature Genetics, 2019).

Dependencies on packages

• STARlong & STARshort - STAR
• samtools - samtools
• bedtools - bedtools
• R package: Biostrings; foreach; doMC; reshape

Installation

1) Obtaining a recent version of R

Clear instructions for different version can be found here: http://cran.fhcrc.org/

2) Install the dependent R packages

# install R package of Biostrings. 
# try http:// if https:// URLs are not supported
> source("https://bioconductor.org/biocLite.R")
> biocLite("Biostrings")

# install packages for parallel computating
> install.packages(c("foreach","doMC","reshape"))

3) Install the STAR2bSMRT R package

git clone https://github.com/zhushijia/STAR2bSMRT.git
R CMD INSTALL -l userFolder STAR2bSMRT

Alternatively, use devtools package

> install.packages("devtools")
> library(devtools)
> install_github("zhushijia/STAR2bSMRT")

Tutorial

See our wiki

Citation

Erin Flaherty, Shijia Zhu, et al., Neuronal impact of patient-specific aberrant NRXN1α splicing, Nature Genetics, 51:1679–1690, 2019. (link)

zhushijia/STAR2bSMRT documentation built on Dec. 18, 2019, 7:37 a.m.