SalmonEISA

Exon/Intron Split Analysis (EISA) pipeline for RNA-Seq C. elegans data using GenomicRanges, GenomicFeatures and Salmon

Index

• Prerequisites
• Usage
• Output

Prerequisites

A Salmon installation:

• Follow this or this.

The following R libraries:

• GenomicRanges, GenomicFeatures, BSgenome.Celegans.UCSC.ce11 and their dependencies.

The following files:

• Cleaned, preprocessed reads in fasta format.
• C. elegans genome file in fasta format: c_elegans.PRJNA13758.WS279.genomic.fa
• C. elegans mature transcripts file in fasta format: c_elegans.PRJNA13758.WS279.mRNA_transcripts.fa
• C. elegans annotation file in GFF3 format: c_elegans.PRJNA13758.WS279.annotations.gff3
• C. elegans gene look-up table containing WORMBASE IDs, gene names and chromosomes. Find it here. Click on Results on then Go.

Usage

Take a look at the headers of each of the following scripts, modify them according to your data and run in order:

1. Build_genes_fasta.R
2. Run_Salmon.sh
3. Build_Rawcounts_EISA.sh
4. SalmonEISA.R

Output

Scatterplot showing ΔExon in relation to ΔIntron for autosomal genes and X genes (+ the Pearson correlation coefficient)