A collection of Python modules & Rscripts for analysis of RNA-seq data for the following publication:
Mutational Landscape of the Transcriptome Offers Putative Targets for Immunotherapy of Myeloproliferative Neoplasms.
Fiorella Schischlik, Roland Jäger, Felix Rosebrock, Eva Hug, Michael Schuster, Raimund Holly, Elisabeth Fuchs, Jelena D Milosevic Feenstra, Edith Bogner, Bettina Gisslinger, Martin Schalling, Elisa Rumi, Daniela Pietra, Gottfried Fischer, Ingrid Faé, Loan Vulliard, Jörg Menche, Torsten Haferlach, Manja Meggendorfer, Anna Stengel, Christoph Bock, Mario Cazzola, Heinz Gisslinger, Robert Kralovics. May 2019, Blood 134(2) DOI: 10.1182/blood.2019000519
- defuse
- tophat-fusion
- SOAPfuse
- gffutils [for annotating fusions]
- pyBigWig [for annotating fusions]
$TMPDIR(path to temporary directory)$NGS_GATK(path to gatk executables)$NGS_PICARD(path to picard executables)
- Annotation and filtering of fusion genes.
- Calling and annotating variants (SNVs & Indels).
- Differential splicing analysis.
- Proposed workflow for neoantigen discovery.
rnaseqlib is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
rnaseqlib 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 Lesser General Public License for more details.