#!/usr/bin/env Rscript

library(polyester)
#fc_matix = matrix(rnorm(37670),ncol=10) writed into "fc_matrix.txt"
rpt=30#read_per_transcript
gtf_f="../input/template.gtf"
genome_path="../input/templateGenome"

fc_matrix=read.table("../../fc_matrix.txt",header=F)
fc_matrix<-as.matrix(fc_matrix)
fc_matrix1 <- fc_matrix[,1]#when two groups, only one column is needed, while three or more groups, number of groups and column should be identical.
simulate_experiment(gtf=gtf_f,seqpath=genome_path,num_reps=c(5,5),reads_per_transcript=rpt,fold_changes=fc_matrix1,paired=T,error_model='illumina4',bias='rnaf',strand_specific=T,seed="12345")