zUMIs.run.yaml

###########################################
#Welcome to zUMIs
#below, please fill the mandatory inputs
#We expect full paths for all files.
###########################################

project: SRR95_raw

sequence_files:
  file1: 
    name: /home/vant/Escritorio/trim/raw_data/SRR12965695/SRR12965695_1.fastq.gz
    base_definition:
      - BC(1-16)
      - UMI(17-28)
  file2:
    name:  /home/vant/Escritorio/trim/raw_data/SRR12965695/SRR12965695_2.fastq.gz
    base_definition:
      - cDNA(1-99)

#reference genome setup
reference:
  STAR_index: /home/vant/Escritorio/genomes/zraw/mus_STAR_idx_NOGTF
  GTF_file: /home/vant/Escritorio/genomes/zraw/Mus_musculus.GRCm38.98.gtf
  additional_files: ~
  additional_STAR_params: ''

#output directory
out_dir: /home/vant/Escritorio/demultiplex/zUMIS/SRR95

#number of processors to use
num_threads: 16
mem_limit: 20

#barcode & UMI filtering options
filter_cutoffs:
  BC_filter:
    num_bases: 1
    phred: 20
  UMI_filter:
    num_bases: 1
    phred: 20

#Options for Barcode handling
barcodes:
  barcode_num: ~
  barcode_file: ~ 
  automatic: yes 
  BarcodeBinning: 1
  nReadsperCell: 100

#Options related to counting of reads towards expression profiles
counting_opts:
  introns: no
  downsampling: '0' 
  strand: 0
  Ham_Dist: 1
  velocyto: no 
  primaryHit: yes 
  twoPass: no 

#produce stats files and plots?
make_stats: yes


#Start zUMIs from stage. Possible TEXT(Filtering, Mapping, Counting, Summarising)
which_Stage: Filtering

#define dependencies program paths
zUMIs_directory: /home/vant/zUMIs
read_layout: SE
samtools_exec: samtools
pigz_exec: pigz
STAR_exec: STAR
Rscript_exec: Rscript