knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "README-" )
2019/11/08:
<!---
2018/11/12:
2018/04/08:
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 (liw@ucla.edu) or Dr. Jessica Li (jli@stat.ucla.edu).
You can install AIDE
from github with:
# install.packages("devtools") devtools::install_github("Vivianstats/AIDE")
aide
requires three input files:
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.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.