AnnOverlappeR

What is AnnOverlappeR?

This is the AnnOverlappeR a tool to find the best overlaps between NCBI EntrezGeneIDs and EnsemblGeneIDs from the Ensembl database using GFF and GTF files from each databases. The tool it self is performing an overlap based on the genomic positions.

Install

Clone the GitHub repo, e.g. with git clone https://github.com/bimbam23/AnnOverlappeR.git

Usage

Rscript AnnOverlappeR.R

Usage: Rscript AnnOverlappeR.R [options]

  --species character
    Species in scientific name (e.g.: homo_sapiens), string, mandatory option

  --output_path character
    output_path, string, optional option

  --numcores integer
    Number of cpus , integer, optional (default 4)

  --download 
    --no-download for no downloads, boolean, mandatory option (default TRUE)

  --latest_ncbi 
    --no-latest_NCBI for no downloads, boolean, mandatory option (default
    FALSE)

  --latest_name character
    latest name found for ncbi latest assembly, string, optional option

  --verbose 
    print messages

  --help 
    Print help message and exit.

  --version 
    Print version information and exit.

Please contact jochen.bick@usys.ethz.ch for comments

Example

Rscript AnnOverlappeR.R -s homo_sapiens --numcores 12 -o ./2018-06-13/ --download --latest_ncbi >hsa_new.out &

Contact

jochen.bick@usys.ethz.ch

Tool dependencies:

library(GetoptLong)
library(GenomicRanges)
library(rtracklayer)
library(XML)
library(pbmcapply)

more dependencies

perl, gzip, wget

Galaxy app

The Galaxy platform is available at https://galaxyproject.org/admin/get-galaxy/. All files have to be copied to the listed folders. The file content of all xml files in the config folder have to be added to the corresponding xml files.

bimbam23 / AnnOverlappeR