AIDE: annotation-assisted isoform discovery and quantification from RNA-seq data

Wei Vivian Li, Jingyi Jessica Li 2022-08-05

Latest News

2019/11/08:

• Version 1.0.0 released!

Introduction

AIDE is a statistical method which identifies full-length mRNA isoforms from a novel perspective: using the likelihood ratio test to find novel isoforms in a stepwise manner given annotated isoforms, by prioritizing and selectively borrowing information from the annotated isoforms. Please refer to our preprint at Biorxiv for detailed description of our method.

Any suggestions on the package are welcome! For technical problems, please report to Issues. For suggestions and comments on the method, please contact Wei ([email protected]) or Dr. Jessica Li ([email protected]).

Installation

You can install AIDE from github with:

# install.packages("devtools")
devtools::install_github("Vivianstats/AIDE")

Quick start

aide requires three input files:

• The GTF file of the genome annotation;
• The BAM file of the RNA-seq sample. The BAM file should be sorted and the index BAI file should be present in the same directory as the BAM file;
• The FASTA file of the genome sequences.

Please also note that aide assumes the above three files use the same format of chromosome names.

The final output of aide is a GTF file named “transcripts.gtf”, which contains the reconstructed transcripts and their corresponding abudance levels. The package has been tested using the GENCODE annotation. This is a basic example which shows how to use the aide function.

aide(gtf_path = "./hg19.gtf",     #full path of the GTF file
    bam_path = "./example.bam",  #full path of the BAM file
    fasta_path = "./hg19.fa",    #full path of the FASTA file
    out_dir = "./",              #output directory of temporary and filnal results
    readLen = 100,               #read length used to calculate ioform effective length
    strandmode = 0,              #library type of the RNA-seq sample
    ncores = 20                  #number of cores used for parallel computation 
    )

Please refer to the package manual for a full list of arguments and detailed usage.