estimate_expression: Estimate expression data from SRA run and reference genome

In momeara/CalCEN: CalCEN: Estimate Co-Expression Networks

Estimate expression data from SRA run and reference genome

Description

Example

Usage

estimate_expression(
  run_accession,
  sra_fname,
  is_paired,
  results_dir,
  logs_dir,
  work_dir,
  reference_genome_path,
  fastq_dump_program,
  rsem_calculate_expression_program,
  bowtie2_path,
  n_threads = 1
)

Arguments

run_accession	identifier for exprsesion run
sra_fname	path to .sra file for the run
is_paired	is it paired end read expression data?
results_dir	path where the results should be stored
logs_dir	path where the logs should be stored
work_dir	path where intermediate data should be stored
reference_genome_path	path to reference genome
fastq_dump_program	path to fastq_dump
rsem_calculate_expression_program	path to rsem-calculate-expression

Details

tag <- "20201209" estimate_expression( run_accession = "SRR513613", sra_fname = "/scratch/maom_root/maom99/maom/CryptoCEN/sra/SRR513613/SRR513613.sra", is_paired = TRUE, results_dir = "intermediate_data/estimated_expression_20201209", results_dir = "intermediate_data/estimated_expression_20201209/logs", work_dir = "/scratch/maom_root/maom99/maom/CryptoCEN/estimated_expression_20201209", reference_genome_path = "/scratch/maom_root/maom99/maom/CryptoCEN/reference_geneome", fastq_dump_program = "

momeara/CalCEN documentation built on Jan. 3, 2023, 7:22 p.m.