zUMIs_yaml_example.yaml

project: SAMPLE
sequence_files:
  file1:
    name: /PATH/SAMPLE_R1.fastq.gz
    base_definition: cDNA(1-61)
  file2:
    name: /PATH/SAMPLE_R2.fastq.gz
    base_definition: BC(1-8)
  file3:
    name: /PATH/SAMPLE_R3.fastq.gz
    base_definition: BC(1-8)
  file4:
    name: /PATH/SAMPLE_R4.fastq.gz
    base_definition:
    - BC(1-8)
    - UMI(9-14)
reference:
  STAR_index: /PATH/STAR_MM99
  GTF_file: /PATH/Mus_musculus.GRCm38.99.gtf
  additional_STAR_params: ''
  additional_files: ~
out_dir: /PATH/SAMPLE_Out
num_threads: 8
mem_limit: 20
filter_cutoffs:
  BC_filter:
    num_bases: 1
    phred: 20
  UMI_filter:
    num_bases: 1
    phred: 20
barcodes:
  barcode_num: ~
  barcode_file: ~
  automatic: yes
  BarcodeBinning: 0
  nReadsperCell: 100
counting_opts:
  introns: yes
  downsampling: '0'
  strand: 1
  Ham_Dist: 0
  velocyto: yes
  primaryHit: no
  twoPass: yes
make_stats: yes
which_Stage: Filtering
Rscript_exec: Rscript
STAR_exec: STAR
pigz_exec: pigz
samtools_exec: samtools
zUMIs_directory: /PATH/zUMIs
read_layout: SE