Analize.R

library(devtools)
library(sleuth)
library(dplyr)
library("biomaRt")

#load annotation from ensembl
ensembl = useMart("ENSEMBL_MART_ENSEMBL",dataset="mmusculus_gene_ensembl", host="www.ensembl.org")
t2g <- biomaRt::getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id", "external_gene_name"), mart = ensembl)
t2g <- dplyr::rename(t2g, target_id = ensembl_transcript_id, ens_gene = ensembl_gene_id, ext_gene = external_gene_name)
#change this directory as your directory
base_dir = "/Volumes/Samsung_T1/RNASeq"

sample_id <- dir(file.path(base_dir,"results"))
kal_dirs <- sapply(sample_id, function(id) file.path(base_dir, "results", id))
kal_dirs <- rev(kal_dirs)
s2c <- read.table(file.path(base_dir,"study_design.txt"), header = TRUE, stringsAsFactors=FALSE)
s2c <- dplyr::select(s2c, sample = run, condition)
s2c <- dplyr::mutate(s2c, path = kal_dirs)
so <- sleuth_prep(s2c, ~ condition, target_mapping = t2g)
so <- sleuth_fit(so)
so <- sleuth_wt(so, which_beta = 'conditionMII')
sleuth_live(so)