ISOSeqNeoAntigen-nf

This workflow uses PacBio ISOSeq reads, exome reads, and RNA-sequencing reads to faciliate the selection of neoantigens that are disease and patient specific.

Summary PacBio ISOSeq discovery

Summary RNAseq:

• Hisat2
• stringtie
• Subread::featurecounts
• limma::voom
• EdgeR::DGEList

Summary Exome seq

• 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):