project: SS3_test_zUMIs
sequence_files:
  file1:
    name: /data/gent/vo/001/gvo00101/projects/Neoantigen_Identification_LungCancer/TMM/Smart-Seq3xpress/FASTQ/reads_for_zUMIs.R1.fastq.gz
    base_definition:
    - cDNA(25-150)
    - UMI(12-21)
    find_pattern: ATTGCGCAATG;2
  file2:
    name: /data/gent/vo/001/gvo00101/projects/Neoantigen_Identification_LungCancer/TMM/Smart-Seq3xpress/FASTQ/reads_for_zUMIs.R2.fastq.gz
    base_definition: 
    - cDNA(1-150)
  file3:
    name: /data/gent/vo/001/gvo00101/projects/Neoantigen_Identification_LungCancer/TMM/Smart-Seq3xpress/FASTQ/reads_for_zUMIs.index.fastq.gz
    - BC(1-10)
reference:
  STAR_index: /data/gent/vo/001/gvo00101/genomes/Hsapiens/hg38-noalt/star/Homo_sapiens.hg38-noalt.gencode_v41.overhang149.STAR.v2.7.6a
  GTF_file: /data/gent/vo/001/gvo00101/genomes/Hsapiens/hg38-noalt/annotation/hg38-noalt.93.gtf
  additional_STAR_params: ~
  additional_files: ~
out_dir: /arcanine/scratch/gent/vo/001/gvo00101/vsc46293/SS3_PBMC_test
num_threads: 48
mem_limit: 60
filter_cutoffs:
  BC_filter:
    num_bases: 1
    phred: 20
  UMI_filter:
    num_bases: 1
    phred: 20
barcodes:
  barcode_num: ~
  barcode_file: /data/gent/vo/001/gvo00101/projects/Neoantigen_Identification_LungCancer/TMM/Smart-Seq3xpress/FASTQ/reads_for_zUMIs.expected_barcodes.txt
  automatic: yes
  BarcodeBinning: 0
  nReadsperCell: 100
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: STAR
pigz_exec: pigz
samtools_exec: samtools
zUMIs_directory: /arcanine/scratch/gent/vo/001/gvo00101/vsc46293/zUMIs