SpliCeAT: Integrated pipeline for detection and quantification of aberrant transcripts with novel splicing events

This repository contains the following Snakemake pipelines and scripts, to be run in this order:

1. Differential splicing detection (ds_detection)
2. Generation of augmented transcriptome (augment_transcriptome)
3. Differential expression analysis (de_analysis)

What you need before starting:

• FASTQ sample files of 2 conditions (control & treatment)
• Aligned BAM files using STAR, indexed using samtools ¹
• Gene annotation (GTF & GFF3) in GENCODE format

Download the respective gene annotations and genome files for the species of interest and place them into a location of your choice:

• A GFF3 gene annotation file (e.g. gencode.vM29.primary_assembly.annotation.gff3). Unzip the file using gunzip tool.
• A GTF gene annotation file (e.g. gencode.vM29.primary_assembly.annotation.gtf.gz).
• A FASTA genome file (e.g. GRCm39.primary_assembly.genome.fa.gz).

You may obtain the annotation files from Gencode (mouse).

Start here:

git clone https://github.com/ys-lim/SpliCeAT.git

Footnotes

1. The pipelines expect RNA-seq alignments/BAM files to be labelled as sample_Aligned.sortedByCoord.out.bam (as in STAR output format). Nevertheless, modifications can be made (at the user's discretion) in the Snakemake rules to account for alignments generated by other tools (e.g. HISAT2). ↩