parameters.yaml

# parameters.yaml specification for FLAM-Seq analysis

experimentName: "FLAMSeq_1"               # Name of Experiment. This will be prefix for generated analysis files.

experiment:
  rawFastq: "/path/to/pacbioreads.fq"     # Define Path to Input PacBio / Nanopore Reads in fastq format
  outputDir: "/path/to/outputDir"         # Define Path to Output dir for writing analysis results. Pipeline will generate of dir is not present.
  genomeIndexDir: "/path/to/STARIndex"    # Define Dir for STARLong Index for Mapping
  annotationGTF: "/path/to/GTFFile"       # GTF File containing gene annotations for assigning reads to genes
  genomeFasta: "/path/to/genomeFasta"     # Genome Fasta File containing genome sequence (that the index was generated from)

software:
  STARlong: "/path/to/STARlong"           # Path to STARlong executable
  featureCounts: "/path/to/featureCounts" # Path to FeatureCounts executable
  nThreads: 8                             # Number of threads for mapping reads