CodonOPT

Calculating codon optimality (cAI or tAI)

Getting Started

You will need a gene and isoform expression matrix with normalized values (ex: TPM)

Prerequisites

R; Perl; bedtools 2.25.0 or higher; Reference files for tRNA adaptiveness (human and mouse available here)

Isoform expression matrix: the first column has to contain the gene symbol as well as the isoform ID separated by one underscore character

ID  rep1  rep2  rep3  rep4  rep5
ACTB_NM_001101  N N N N N

Step 1: Select highest expressed isoform

Run this script to select the isoform with highest expression for each gene. All the reference files needed for human and mouse are in the respective folders. Note: the reference annotation files contain the CDS regions only of the coding genes

source_step1.bash YOUR_ISOFORM_EXP.tsv YOUR_CDS_REFERENCE.bed GENE_NAME_REF

the output will be a file named coding_renamed_one_iso.bed

Step 2: Calculate tAI (tRNA adaptiveness index, based on tRNA copy numbers in genome)

Run this script and generate a codon based and gene based tAI output

Reference fasta not provided, select apropriate tRNA adaptiveness file

perl new_codonbias.pl YOUR_REF.fa tRNA_adaptiveness_SPECIES.txt coding_renamed_one_iso.bed output_tAI_per_codon.txt > gene_tAI.tsv

Step 3: Select top 10% expressed genes

Run this R script to identify the top 10% expressed genes and filter the output of step 2. The result is a file named top_expressed_output_tAI_per_codon.txt

Rscript source_step3.R YOUR_GENE_EXPRESSION.tsv output_tAI_per_codon.txt

Step 4: Calculate cAI (codon adaptation index, Sharp 1987)

Run this R script to calculate cAI. Depends on the filtered codon output generated in step 3.

Rscript source_step4.R codons_AA.txt top_expressed_output_tAI_per_codon.txt

perl ~/bin/new_codonbias.pl YOUR_REF.fa cAI.tsv coding_renamed_one_iso.bed output_cAI_per_codon.txt > gene_cAI.tsv