RNA-Seq is the predominant method of profiling the transcriptome. The signature of altered splicing kinetics can be detected in many transcriptomic contexts. What does this signature indicate in terms of RNA biology?
Here, we aim to quantify partially spliced mRNA-biogenesis intermediates from RNA-seq data. We will refer to these as SpIriTs (splicing intermediary transcripts). Our pipeline, which detects and quantifies SpIriTs, will be referred to as the Clairvoyant RNA Observer (ClaiRO)
# Projects
*`core-ExoDUs` (Exon Defining Units) contains scripts which analyse at the coordination of splicing around the casette exons of protein coding genes
*`core-magic` represents the newest Pluto build, identifying global partial splicing, independanlty of fragment size or location
*`core` (deprecated) represents the archaic Pluto series scripts, which identified transcriptome-wide partial splicing
* Note: Dependencies are pacakged into the ClaiRO git repository, such that the repo should work instantly on NCI's Gadi HPC. For users running ClaiRO on local machines or other clusters, scripts may need to be adjusted in order to access local installations.
# Usage (ExoDUs)
* Clone into the repository
* Make an index using /core-ExoDUs/make-ExoDUs-index.sh
* Analyse an alingment (BAM format) using characterise-ExoDUs.sh
ExoDUs will output a tab-delimited list of cassette exons, event types (fully-spliced, fully-unspliced, forward exon spliced, back exon spliced), and counts for each detected event.
ClaiRO is a low-bias method to detect and quantify exon-defining units from paired-end RNA-Seq alignments
# Dependencies
ClaiRO relies on several packages. Please ensure these are available within your PATH.
* Bedtools (Quinlan, 2014)
* Samtools (Li et al., 2009)
* Picard (Broad Institute, 2019)
* Subread FeatureCounts (Liao and Shi, 2019)
* GNU Parallel (Tange, 2018)
# Installation
ClaiRO is a collection of scripts and does not require installation directly.
To clone into the repository, use the following command:
