This workflow uses PacBio ISOSeq reads, exome reads, and RNA-sequencing reads to faciliate the selection of neoantigens that are disease and patient specific.
- Hisat2
- stringtie
- Subread::featurecounts
- limma::voom
- EdgeR::DGEList
- bwa mem
- bcftools mpileup
- bcftools filter
- bcftools annotate
- annotate_variation.pl
- table_annovar.pl
- http://shiva.rockefeller.edu/SeqTailor/index_protein.php
- Filter for SIFT_prediction: deleterious, Polyphen2_HDIV_prediction: deleterious (PP_D) and probable deleterious (PP_P):