Bio::ViennaNGS ============== Bio::ViennaNGS is a collection of Perl modules for Next-Generation Sequencng (NGS) analysis. It comes with a set of utility programs for accomplishing routine tasks often required in NGS data processing. The utilities serve as reference implementation of the routines implemented in the library and reside within the 'scripts' folder: bam_split.pl: Split (paired-end and single-end) BAM alignment files by strand and compute statistics. Optionally create BED output, as well as normalized bedGraph and bigWig files for coverage visualization in genome browsers (see dependencies on third-patry tools below). bam_uniq.pl Extract unique and multi mapping reads from BAM alignment files and create a separate BAM file for both uniqe (.uniq.) and multi (.mult.) mappers. gff2bed.pl: Convert RefSeq GFF3 annotation files to BED12 format. Individual BED12 files are created for each feature type (CDS/tRNA/rRNA/etc.). Tested with RefSeq bacterial GFF3 annotation. motiffinda.pl: Find motifs in annotated sequences. The motif can be provied as regex. DEXSeq_gff2bed.pl: Convert flat GFF file produced by DEXSeq's dexseq_prepare_annotation.py to BED6 for easy UCSC integration. normalize_multicov.pl: Compute normalized expression data in TPM/RPKM from (raw) read counts in bedtools multicov format. TPM reference: Wagner et al, Theory Biosci. 131(4), pp 281-85 (2012) splice_site_summary.pl: Identify and characterize splice junctions from RNA-seq data by intersecting them with annotated splice junctions. newUCSCdb.pl: Create a new genome database for a locally installed instance of the UCSC genome browser. Based on http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database INSTALLATION To install this module type the following: perl Makefile.PL make make test make install DEPENDENCIES This module requires these other modules and libraries: Bio::Perl >= 1.006924 Bio::DB::Sam >= 1.39 File::Basename File::Temp IPC::Cmd Pod::Usage Carp The following modules are required for the utility programs inside the 'scripts' folder: Bio::ViennaNGS::AnnoC Bio::ViennaNGS::SpliceJunc Bio::ViennaNGS::UCSC Computation of BigWig files from BAM is accomplished via two calls to third-party tools internally. genomeCoverageBed from the BEDtools suite (http://bedtools.readthedocs.org/en/latest/content/tools/genomecov.html) is used to create a BedGraph coverage file at first place. In a second step, the BedGraph is converted to BigWig by bedGraphToBig, a UCSC Genome Browser utility (http://hgdownload.cse.ucsc.edu/admin/exe/). Make sure that both third-party utilities (genomeCoverageBed and bedGraphToBigWig) are available on your system. AUTHORS Michael T. Wolfinger Florian Eggenhofer Joerg Fallmann COPYRIGHT AND LICENCE Copyright (C) 2014 Michael T. Wolfinger This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.12.4 or, at your option, any later version of Perl 5 you may have available. This program 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. See the GNU General Public License for more details.