STARlong and STARshort based Single Molecule Real Time Iso-Seq analysis
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).
- STARlong & STARshort - STAR
- samtools - samtools
- bedtools - bedtools
- R package: Biostrings; foreach; doMC; reshape
Clear instructions for different version can be found here: http://cran.fhcrc.org/
# 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"))
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")
See our wiki
Erin Flaherty*, Shijia Zhu*, et al., Neuronal impact of patient-specific aberrant NRXN1α splicing, Nature Genetics, 51:1679–1690, 2019. (link)