config.yaml

# Test dataset
Test:
  read_length: 100
  fastq_path: "rn7/Test/fastq"
  paired_end: false
  geno_dataset: "Brain"

# IL, LHb, NAcc, OFC, and PL datsets
IL:
  read_length: 100
  fastq_path: "fastq/IL_LHb_NAcc_OFC_PL"
  paired_end: false
  geno_dataset: "IL_LHb_NAcc_OFC_PL"
LHb:
  read_length: 100
  fastq_path: "fastq/IL_LHb_NAcc_OFC_PL"
  paired_end: false
  geno_dataset: "IL_LHb_NAcc_OFC_PL"
NAcc:
  read_length: 100
  fastq_path: "fastq/IL_LHb_NAcc_OFC_PL"
  paired_end: false
  geno_dataset: "IL_LHb_NAcc_OFC_PL"
OFC:
  read_length: 100
  fastq_path: "fastq/IL_LHb_NAcc_OFC_PL"
  paired_end: false
  geno_dataset: "IL_LHb_NAcc_OFC_PL"
PL:
  read_length: 100
  fastq_path: "fastq/IL_LHb_NAcc_OFC_PL"
  paired_end: false
  geno_dataset: "IL_LHb_NAcc_OFC_PL"

# Eye dataset
Eye:
  read_length: 150
  fastq_path: "fastq/Eye"
  paired_end: true
  geno_dataset: "Eye"

# BLA, NAcc2, and PL2 samples from u01_suzanne_mitchell
# Note: half of NAcc2 samples are single-end. Run STAR and RSEM for single-end and
# paired-end separately using different fastq_map.txt and rat_ids.txt files.
# Then continue with combined rat_ids.txt and fastq_map.txt files. When running single-end, change
# paired_end to false below.
BLA:
  read_length: 100
  fastq_path: "fastq/BLA_NAcc2_PL2"
  paired_end: true
  geno_dataset: "BLA_NAcc2_PL2"
NAcc2:
  read_length: 100
  fastq_path: "fastq/BLA_NAcc2_PL2"
  paired_end: true
  geno_dataset: "BLA_NAcc2_PL2"
PL2:
  read_length: 100
  fastq_path: "fastq/BLA_NAcc2_PL2"
  paired_end: true
  geno_dataset: "BLA_NAcc2_PL2"

# Adipose and Liver dataset
Adipose:
  read_length: 76
  fastq_path: "fastq/Adipose_Liver/Fat"
  paired_end: false
  geno_dataset: "Adipose_Liver"
Liver:
  read_length: 126
  fastq_path: "fastq/Adipose_Liver/Liver"
  paired_end: true
  geno_dataset: "Adipose_Liver"

# Whole brain hemisphere dataset
Brain:
  read_length: 101
  fastq_path: "../bulk/wb/fastq"
  paired_end: true
  geno_dataset: "Brain"

# RMTg dataset
RMTg:
  read_length: 151
  fastq_path: "fastq/RMTg"
  paired_end: true
  geno_dataset: "RMTg"