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README.md

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In order to configure your analysis, make changes to config.yaml.

  1. SAMPLES: A tab-separated file with the following example should be provided to specify the samples:
sample condition type
ETOH.R1 EtOH RNA
ETOH.R2 EtOH RNA
ETOH.R3 EtOH RNA
DHT.R1 DHT RNA
DHT.R2 DHT RNA
DHT.R3 DHT RNA
INPUT DNA

sample: Sample name

condition: Treatment condition (blank if none; blank for DNA)

type: Sample type (RNA or DNA)

  1. UNITS: A tab-separated file with the following example should be provided to specify the units (replicates or lanes):
sample unit fq1 fq2
ETOH.R1 1 reads/EM_LNCaP_R1_EtOH_L1_1.fq.gz reads/EM_LNCaP_R1_EtOH_L1_2.fq.gz
ETOH.R2 1 reads/EM_LNCaP_R2_EtOH_L1_1.fq.gz reads/EM_LNCaP_R2_EtOH_L1_2.fq.gz
ETOH.R3 1 reads/EM_LNCaP_R3_EtOH_L1_1.fq.gz reads/EM_LNCaP_R3_EtOH_L1_2.fq.gz
ETOH.R3 2 reads/EM_LNCaP_R3_EtOH_L2_1.fq.gz reads/EM_LNCaP_R3_EtOH_L2_2.fq.gz
DHT.R1 1 reads/EM_LNCaP_R1_DHT_L1_1.fq.gz reads/EM_LNCaP_R1_DHT_L1_2.fq.gz
DHT.R2 1 reads/EM_LNCaP_R2_DHT_L1_1.fq.gz reads/EM_LNCaP_R2_DHT_L1_2.fq.gz
DHT.R3 1 reads/EM_LNCaP_R3_DHT_L1_1.fq.gz reads/EM_LNCaP_R3_DHT_L1_2.fq.gz
INPUT 1 reads/NL18_L2_1.fq.gz reads/NL18_L2_2.fq.gz

sample: Sample name (same as in samples.tsv)

unit: Unit no

fq1: Path to the 1st FASTQ file

fq2: Path to the 2nd FASTQ file

  1. PRIMERS: A tab-separated file with the following specificiations (and example row) should be provided to specify the regions of analysis:
Region name Forward primer Reverse primer Chromosome Start End
overlapped_read_114 AGCGCGGCTTAGTGA TACCAGGAGACTATTTCCAACA chr8 6456903 6457213

This file shouldn't have a header. The primers should be 5' to 3' and the positions should be BED-like (0-based).

  1. REF

    1. FA: Path to the FASTA file of the reference genome
    2. BWA_IDX: Path to the BWA index files (prefix)
    3. FIXED: Path to the FASTA file matching the wild type plasmids (or the same as FA)
  2. SEQ

    1. UMI1_LEN: Length of the 5' UMI
    2. UMI2_LEN: Length of the 3' UMI
    3. EXPECTED_TLEN: Template (insert) length of the plasmids (excluding UMIs but including primers)