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cryptex's Introduction

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

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