## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#    library(ORFik)                        # This package
#    # Here the default values are shown:
#    where_to_save_config <- "~/bio_data/ORFik_config.csv"
#  
#    parent_folder <- "~/bio_data/"
#    fastq.dir <- file.path(parent_folder, "raw_data")
#    bam.dir <- file.path(parent_folder, "processed_data")
#    reference.dir <- file.path(parent_folder, "references")
#    config.save(where_to_save_config,
#                fastq.dir, bam.dir, reference.dir)

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#    config()

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#    conf <- config.exper(experiment = "CHALMERS_Yeast", # short experiment info: here I used author + species
#                       assembly = "Yeast_SacCer3", # Reference folder
#                       type = c("RNA-seq")) # fastq and bam type
#    conf

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#  
#  info <- download.SRA.metadata("SRP012047", outdir = conf["fastq RNA-seq"])
#  # Let's take 2 first runs in this experiment:
#  info <- info[1:2,]

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#  # Subset
#  # 18 MB, ~ 40 sec download time ->
#  download.SRA(info, conf["fastq RNA-seq"], subset = 50000)
#  
#  # Or you could do the full libraries
#  # 1.6 GB, ~ 100 sec download time
#  # (Full size files have faster MB/s download speed than subsets) ->
#  # download.SRA(info, conf["fastq RNA-seq"])

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#  organism <- info$ScientificName[1]
#  is_paired_end <- all(info$LibraryLayout == "PAIRED")

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#    annotation <- getGenomeAndAnnotation(
#                        organism = organism,
#                        output.dir = conf["ref"],
#                        assembly_type = "toplevel"
#                        )

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#    annotation <- getGenomeAndAnnotation(
#                        organism = organism,
#                        genome = TRUE, GTF = TRUE,
#                        phix = TRUE, ncRNA = TRUE, tRNA = TRUE, rRNA = TRUE,
#                        output.dir = conf["ref"],
#                        assembly_type = "toplevel"
#                        )

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#    gtf <- "/path/to/local/annotation.gtf"
#    genome <- "/path/to/local/genome.fasta"
#    makeTxdbFromGenome(gtf, genome, organism = "Saccharomyces cerevisiae")

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#    txdb <- "/path/to/local/annotation.gtf.db"
#    cage <- "/path/to/CAGE.ofst" # Can be bed, wig etc (ofst is fastest)
#    reassigned_txdb <- assignTSSByCage(txdb, cage)
#    AnnotationDbi::saveDb("/path/to/local/annotation_cage.db")

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#    txdb <- "/path/to/local/annotation.gtf.db"
#    reassigned_txdb <- assignTSSByCage(txdb, cage = NULL, pseudoLength = 100)
#    AnnotationDbi::saveDb(reassigned_txdb,
#                          "/path/to/local/annotation_pseudo_leaders.db")
#    leaders <- loadRegion(reassigned_txdb, "leaders")

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#  index <- STAR.index(annotation)

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#  alignment <-
#    STAR.align.folder(conf["fastq RNA-seq"], conf["bam RNA-seq"], index,
#                      paired.end = is_paired_end,
#                      steps = "tr-ge", # (trim needed: adapters found, then genome)
#                      adapter.sequence = "auto",
#                      max.cpus = 30, trim.front = 3, min.length = 20)

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#  dir.create("~/UMIandTrimmed")
#  system(paste(install.fastp(),
#               "-i", "~/sample1.fastq.gz",
#               "-o", "~/UMIandTrimmed/sample1.UMIandTrimmed.fastq.gz"
#               "--adapter_sequence=AGATCGGAAGAGC",
#               "--umi",
#               "--umi_loc", "read1",
#               "--umi_len", 12))
#  # Read fastp documentation for info about umi arguments

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#  alignment <-
#    STAR.align.folder(conf["fastq RNA-seq"], conf["bam RNA-seq"], index,
#                      paired.end = is_paired_end,
#                      steps = "tr", # (Only trim)
#                      adapter.sequence = "auto",
#                      max.cpus = 30, trim.front = 3, min.length = 20)
#  trimmed_files <- file.path(conf["bam RNA-seq"], "trim")
#  # Check that trimmed reads are average < 50 bases, else collapsing makes little sense for speedup.
#  trim_table <- ORFik:::trimming.table(trimmed_files)
#  stopifnot(all(trim_table$trim_mean_length < 50))
#  trimmed_fastq <- list.files(path = trimmed_files, pattern = "fastq", full.names = TRUE)
#  ORFik::collapse.fastq(files = trimmed_fastq, outdir = file.path(conf["bam Ribo-seq"], "collapsed") # Collapse all files in trim folder
#  # Then align using collapsed reads
#  alignment <-
#    STAR.align.folder(trimmed_files, conf["bam RNA-seq"], index,
#                      paired.end = is_paired_end,
#                      steps = "ge", # (Only genome alignment from collapsed)
#                      max.cpus = 30, min.length = 20)

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#  index <- STAR.index(annotation, max.ram = 20, SAsparse = 2)

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#  STAR.align.folder(conf["fastq RNA-seq"], conf["bam RNA-seq"], index,
#                      max.cpus = 4) # Reduce cores to 4 usually works for most systems

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#  STAR.align.folder(conf["fastq RNA-seq"], conf["bam RNA-seq"], index,
#                      max.cpus = 4, steps = "tr-ge", resume = "ge") # Resume ge using completed tr

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#  txdb_file <- paste0(annotation["gtf"], ".db") # Get txdb file, not raw gtf
#  fa <- annotation["genome"]
#  create.experiment(exper = "yeast_exp_RNA",
#                    dir = paste0(conf["bam RNA-seq"], "/aligned/"),
#                    txdb = txdb_file,
#                    fa = fa,
#                    organism = organism,
#                    viewTemplate = FALSE,
#                    pairedEndBam = is_paired_end # True/False per bam file
#                    )

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#  df <- read.experiment("yeast_exp_RNA")

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#    QCreport(df)

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#    remove.experiments(df) # Remove loaded libraries
#    convertLibs(df, type = "ofst")

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#    remove.experiments(df)
#    convertLibs(df, type = "wig")

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#    remove.experiments(df)
#    outputLibs(df, type = "ofst")

## ----eval = FALSE, echo = TRUE, message = FALSE-------------------------------
#    mrna <- countTable(df, region = "mrna", type = "fpkm")
#    cds <- countTable(df, region = "cds", type = "fpkm")
#    ratio <- cds / mrna

