project: 10x
sequence_files:
  file1:
    name: /data/neuron_1k_v3_S1_L001_R1_001.fastq.gz
    base_definition:
    - BC(1-16)
    - UMI(17-28)
  file2:
    name: /data/neuron_1k_v3_S1_L001_R2_001.fastq.gz
    base_definition: cDNA(1-90)
  file3:
    name: /data/neuron_1k_v3_S1_L001_I1_001.fastq.gz
    base_definition: BC(1-8)
reference:
  STAR_index: /data/star
  GTF_file: /data/GCF_000001635.27_GRCm39_genomic.gff
  additional_STAR_params: ''
  additional_files: ~
out_dir: /data/output
num_threads: 32
mem_limit: 62
filter_cutoffs:
  BC_filter:
    num_bases: 2
    phred: 25
  UMI_filter:
    num_bases: 2
    phred: 25
barcodes:
  barcode_num: ~
  barcode_sharing: /data/shared_i7_barcodes.txt
  automatic: no
  BarcodeBinning: 0
  nReadsperCell: 50
counting_opts:
  introns: yes
  downsampling: '0'
  strand: 0
  Ham_Dist: 0
  velocyto: no
  primaryHit: yes
  twoPass: yes
make_stats: yes
which_Stage: Filtering
Rscript_exec: Rscript
STAR_exec: /usr/bin/STAR-2.7.10b/source/STAR
pigz_exec: pigz
samtools_exec: samtools