NAME

Pipeline.pl - An example pipeline for the ViennaNGS toolbox

SYNOPSIS

./Pipeline.pl [-r STRING]

DESCRIPTION

This script is a showcase for the usage of ViennaNGS in a real NGS example. We start from a file containing ENSEMBL annotation information for human protein-coding genes, which have a read pileup of at least 1001 reads in an ENCODE dataset mapped with segemehl. We are insterested in finding sequence motifs in close proximity to the gene start (50nt upstream, 10nt into the gene).

The first step is to initialize some variables and generate a chromosome-sizes hash.

Generate a Bio::ViennaNGS::FeatureChain object

The bed file of interest is parsed, a feature array is generated and passed on to Bio::ViennaNGS::FeatureChain, which creates a new Moose Object of type FeatureChain, containing the original bed entries

OPTIONS

--rpath -r

The command line option -r should be given a path to the R-lib directory containing ggplot2, which is needed for the MEME_xml_motif_extractor.pl, otherwise this script will fail.

--help -h

Print short help

--man

Prints the manual page and exits

AUTHOR

Joerg Fallmann <joerg.fallmann@univie.ac.at>