2013Dec19.R

# do RNA-seq simulation to see if it will work!
# AF 19 december 2013

library(devtools)
##### ADD PASSWORD WHEN RUNNING
install_github('ballgown_paper','alyssafrazee',subdir='simde',password='')
library(simde)

fasta_file = 'chr22.fa'
count_transcripts(fasta_file) #918 transcripts
setwd('simulated_data')

# 918 transcripts
# let's make 92 of them DE
# at 2x and 5x
# half in each group
# and shuffle them around
fc = c(rep(2, 23), rep(5, 23), rep(0.5, 23), rep(0.2, 23), rep(1, 826))
set.seed(651)
fc = sample(fc)

## do simulation:
simulate_experiment(fasta_file, num_reps = 15, outprefix = 'sim', 
    model = multinomial, fold_changes = fc)