project: ipsiVcontraSS3
sequence_files:
  file1:
    name: /mnt/heintz-bambi3/WORK/bfait/cases/ipsiVcontra/realDeal/Undetermined_S0_R1_001.fastq.gz
    base_definition:
    - cDNA(23-300)
    - UMI(12-19)
    find_pattern: ATTGCGCAATG
  file2:
    name: /mnt/heintz-bambi3/WORK/bfait/cases/ipsiVcontra/realDeal/Undetermined_S0_I1_001.fastq.gz
    base_definition: BC(1-8)
  file3:
    name: /mnt/heintz-bambi3/WORK/bfait/cases/ipsiVcontra/realDeal/Undetermined_S0_I2_001.fastq.gz
    base_definition: BC(1-8)
reference:
  STAR_index: /mnt/heintz-bambi3/WORK/bfait/genomes/vM6STAR
  GTF_file: /mnt/heintz-bambi3/WORK/bfait/genomes/gencode.vM6.annotation.gtf
  additional_STAR_params: '--clip3pAdapterSeq CTGTCTCTTATACACATCT'
  additional_files: /mnt/heintz-bambi3/WORK/bfait/cases/ipsiVcontra/realDeal/sfGFP.fasta
out_dir: /mnt/heintz-bambi3/WORK/bfait/cases/ipsiVcontra/realDeal/output
num_threads: 4
mem_limit: 8
filter_cutoffs:
  BC_filter:
    num_bases: 3
    phred: 20
  UMI_filter:
    num_bases: 2
    phred: 20
barcodes:
  barcode_num: ~
  barcode_file: /mnt/heintz-bambi3/WORK/bfait/cases/ipsiVcontra/realDeal/ipsiVcontraWhiteList.txt
  automatic: no
  BarcodeBinning: 1
  nReadsperCell: 500
counting_opts:
  introns: yes
  downsampling: '0'
  strand: 0
  Ham_Dist: 1
  velocyto: no
  primaryHit: yes
  twoPass: no
make_stats: yes
which_Stage: Filtering
Rscript_exec: Rscript
STAR_exec: STAR
pigz_exec: pigz
samtools_exec: samtools