Epi-Seq: Bioinformatics pipeline for predicting tumor specific epitopes from RNA-Seq data
Epi-Seq is a multi-step bioinformatics analysis pipeline that starts from the raw RNA-Seq tumor reads, and produces a set of predicted tumor-specific expressed epitopes. It integrates several bioinformatics tools from the NGSTools and IsoEM packages developed in the Mandoiu lab, including the SNVQ algorithm for calling mutations from RNA-Seq data and the RefHap single individual haplotyping algorithm, as well as the NetMHC 3.0 epitope prediction algorithm developed at the Center for Biological Sequence Analysis, Technical University of Denmark. See the README.TXT file for installation instructions and full dependencies.
Epi-Seq source code and distribution
- Online batch primer design to resequence somatic C57BL mutations in mm9 or mm10 genome coordinates, and BALBc mutations in mm9 coordinates.
Acknowledgment and Disclaimer
This material is based upon work supported in part by the National Science Foundation under Grants No. IIS-0546457, DBI-0543365, and IIS-0916948, and by the USDA National Institute of Food and Agriculture under award #2011-67016-30331. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the funding agencies.