create.rnaseqc.script: A method
In decusInLabore/biologicSeqTools2: Seq Analysis Helper Functions

create.rnaseqc.script

R Documentation

A method

Description

Method description

Usage

create.rnaseqc.script(
  df.design,
  sample.column = "sample.id",
  project.code = "p103",
  project = "SB_RNAseqQC",
  basedataDir =
    "/camp/stp/babs/working/boeings/Projects/103_VTL_ES_RNA_seq_BAFF_timecourse_hs/workdir/RSEM/Ensembl",
  bam.suffix = "STAR.genome.bam",
  GTFfile =
    "/camp/stp/babs/working/data/genomes/homo_sapiens/ensembl/GRCh38/release-86/gtf/Homo_sapiens.GRCh38.86.rnaseqc.gtf",
  rRNAfile =
    "/camp/stp/babs/working/data/genomes/homo_sapiens/ensembl/GRCh38/release-86/gtf/Homo_sapiens.GRCh38.86.rRNA.list",
  genome.fa =
    "/camp/stp/babs/working/data/genomes/homo_sapiens/ensembl/GRCh38/release-86/genome/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa",
  refFlatFile = "",
  ribosomalIntervalList = "",
  bedFile = "",
  paired.end = FALSE,
  strandSpecific = TRUE
)