nh13 / CryptEx

Scripts used to discover and quantify non-annotated cryptic splicing in RNA-seq data

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