RNAcentral Genome Mapper

This repository is archived and its functionality has been replaced by the new blat-based genome mapping pipeline.

About

This repository contains the code that is used internally for mapping RNAcentral sequences to their genomic locations based on the underlying INSDC accessions.

Example:

AL133244.1 (15569:15681) corresponds to human chromosome 2 (32945339:32945451).

Uses Ensembl Perl API and Bioperl.

Requirements

DBD::mysql for connecting to Ensembl
DBD::Oracle for connecting to RNAcentral

Installation

# clone this repo
git clone https://github.com/RNAcentral/genome-mapper.git

# initialise submodules
cd genome-mapper
git submodule init
git submodule update

# optional: checkout the desired Ensembl branch

# optional: check that Ensembl connection is working
source setup.sh
perl ensembl/misc-scripts/ping_ensembl.pl

# make a copy of the params script and add the connection details
cp scripts/params_template.sh scripts/params.sh

The connection parameters for the RNAcentral database are stored in scripts/params.sh (excluded from version control).

Usage

source setup.sh
perl genome_mapper.pl -s Homo_sapiens