dea_tx2gene_from_gff3.R

In sarangian/deaRscripts: Differential Expression Analysis based on the read count data generated by either of Salmon, Kallisto, featureCounts and perform statistical analysis to discover quantitative changes in expression levels between two different experimental groups

#!/usr/bin/env Rscript
suppressMessages(library(readr))
suppressMessages(library(optparse))
suppressMessages(library(tximport))
suppressMessages(library(GenomicFeatures))
option_list = list(
  make_option(c("-g", "--gff3"), type="character", default=NULL,help="gff3 file path", metavar="character"),
  make_option(c("-o", "--out"), type="character", default=NULL,help="tx2gene file name (.csv)", metavar="character")
 );
opt_parser = OptionParser(option_list=option_list);
opt = parse_args(opt_parser);
txdb <- makeTxDbFromGFF(file=opt$gff3)
txdf <- select(txdb, keys(txdb, "TXNAME"), "GENEID", "TXNAME")
txdf$GENEID <-paste(txdf$TXNAME,txdf$GENEID, sep = "*")
write.table(txdf,opt$out, sep=",", col.names = TRUE, row.names = FALSE, quote=FALSE)