NAME

Bio::ViennaNGS::Tutorial - A collection of basic tutorials demonstrating of the core components and features of the Bio::ViennaNGS suite

DESCRIPTION

The Bio::ViennaNGS tutorial is a collection of fully documented pipeline scripts that have been built as a showcase for the usage of the Bio::ViennaNGS distribution with real NGS data.

DISCLAIMER

Many example pipelines covered here work and depend on fairly large real world NGS data sets in the gigabyte scale. Be prepared that each tutorial takes a couple of hours of CPU time to finish. When running the scripts locally you need to ensure that your system has enough hardware resources available.

DATA DOWNLOAD

All input data required for the individual tutorial pipelines can be downloaded from the ViennaNGS data repository.

TUTORIALS

Tutorial 00: Inferring detailed mapping statistics from BAM files

Tutorial 01: Computation and analysis of sequence motifs in close proximity to gene starts in a set of ENCODE human protein coding genes

Tutorial 02: Extraction and manipulation of strand-specific ENCODE RNA-seq data and automatic generation of coverage profiles

Tutorial 03: Automatic generation of UCSC genome browser Track Hubs for visualization of ENCODE RNA-seq data

AUTHORS

Michael T. Wolfinger <michael@wolfinger.eu>

Joerg Fallmann <fall@tbi.univie.ac.at>

Florian Eggenhofer <florian.eggenhofer@tbi.univie.ac.at>

Fabian Amman <fabian@tbi.univie.ac.at<gt>

COPYRIGHT AND LICENSE

Copyright (C) 2014-2015 Michael T. Wolfinger <michael@wolfinger.eu>

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.10.0 or, at your option, any later version of Perl 5 you may have available.

This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.