Within this chapter, we utilize the nextNEOpi pipeline to conduct an analysis of genomic and transcriptomic data derived from several biopsy sites of three patients with lung tumors (Sharma et al. 2019). This investigation illustrates how nextNEOpi aids in detecting potential canonical neoantigens, neoantigens arising from fusions, and other cancer-related attributes crucial for immunotherapy.
This repository houses a selection of scripts essential for replicating the analysis outlined in the chapter:
The list of SRA sample accessions (SRR_Acc_List.txt) and the associated metadata (SraRunTable.txt).
A Nextflow script (SRA_download.nf), designed to download the raw sequencing data using the SRA toolkit, with input from the SRR_Acc_List.txt file, and its accompanying Nextflow configuration file (nextflow.config). You may need to modify the nextflow.config to accommodate your computational environment.
An R script (Sharma_nextneopi_samplesheet.R), which processes the SraRunTable.txt file to generate the CSV input sample sheet for nextNEOpi, plus an example sample sheet (Sharma_nextneopi_samplesheet.csv). Installation of the dplyer, readr, and stringr R packages is required for this script.
An additional R script for visualizing the analysis outcomes (Sharma_nextneopi_analysis.R). This script necessitates the installation of several R packages: stringr, readr, ggplot2, dplyr, patchwork, vegan, and DiversitySeq (available at https://sysbiobig.dei.unipd.it/software/diversityseq/).
For detailed instructions on replicating the analysis, please consult the chapter itself.