GitHub - jackhump/CryptEx: Scripts used to discover and quantify non-annotated cryptic splicing in RNA-seq data (original) (raw)
CryptEx
A set of scripts that identify, quantify and classify cryptic splicing in RNA-seq data.
CryptEx paper is now published!
Quantitative analysis of cryptic splicing associated with TDP-43 depletion
Jack Humphrey, Warren Emmett, Pietro Fratta, Adrian M. Isaacs and Vincent Plagnol
https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-017-0274-1
Pre-requisites:
- BEDTools
- R (>= 3.1)
- SAMtools
- STAR - to align fastq files and generate splice junctions
R packages:
- BioStrings
- DEXSeq
- data.table
- dplyr
- GenomicRanges
- ggplot2
- gridExtra
- gplot
- optparse
- plyr
- stringr
- tidyr