RNA-seq support in AltAnalyze
Nathan Salomonis
provides new methods for the import and analysis of whole-genome RNA
sequencing data in addition to ongoing support of Affymetrix exon,
junction and gene arrays. Users with RNA sequence data can import
pre-aligned junction summaries in the form of junction BED files
produced by several junction mapping tools (e.g., TopHat, HMMSplicer,
SpliceMap) to identify known and novel exon-inclusion events with
reciprocal changes in exon-junction expression across one or more
experimental conditions. As with other supported platforms, AltAnalyze
will annotate these results at the level of associated and predicted
alternative splicing events (e.g., mutually-exclusive, alternative
splice-site, intron-retention, alternative promoter, trans-splicing),
known exons (Ensembl/UCSC), optimally aligning mRNA and protein
isoforms and assess the functional impact on domain/motif/microRNA
binding site inclusion.
Since the algorithms and annotations are standardized between
technologies, users can directly compare their results across
platforms (e.g., RNA sequencing and junction arrays) or across
species. For visualization in the associated program DomainGraph,
identified alternative exons are converted to compatible identifiers
for this software (see documentation:
http://altanalyze.org/AltAnalyze_Manual.pdf). A tutorial and sample
input files are available for analysis at:
http://code.google.com/p/altanalyze/wiki/Tutorial_AltExpression_RNASeq
Although this version has been tested extensively in house, we
appreciate your further evaluation and feedback as this is currently
deemed a beta version. If you have questions, problems or feature
requests related to this software, please do not hesitate to contact
us.
Best Regards,
AltAnalyze Development Team
http://www.altanalyze.org
http://code.google.com/p/altanalyze/
http://code.google.com/p/altanalyze/wiki/ContactUs
