SPACE-Tag-preprocessing/config.yaml at main · nygctech/SPACE-Tag-preprocessing · GitHub

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##########################
# Input files (required) #
##########################

sample_fastqs:
  example:
    # Read 1 (16bp Visium barcode + 12bm UMI)
    R1: data/example_r1.fastq.gz
    # Read 2 (gDNA only)
    R2: data/example_r2.fastq.gz

sample_alignment_jsons:
  # Path to SpaceRanger fiducial alignment json - if you want to do automated alignment (currently not implemented), put 'none'
  example: data/example.json

### Whether to do full run for processing or just debug/QC
# options: 'processing', 'debug'
run_type: 'processing'

# Path and prefix for bowtie2 genome reference
ref: path/to/ref/and/prefix

###########################################
# Configuration options for all run types #
###########################################

### single-end or paired-end mode
# options: 'se', 'pe'
mode: 'se'

# structure of read 1
# if using STCT, default is '(?P<cell_1>.{16})(?P<umi_1>.{12})'
r1_format: '(?P<cell_1>.{16})(?P<umi_1>.{12})'

# Whether to use UMIs for deduplication
umi_dedup: False

### Options for MACS2 peak calling
# FDR threshold for peak calling
macs2_fdr: 0.05

# Effective genome size
# Defaults for species:
#   hs: 2.7e9
#   mm: 1.87e9
#   ce: 9e7
#   dm: 1.2e8
macs2_genomesize: 1.87e9

####################################################
# Configuration options for spatial processing run #
####################################################

# Remove artifact pA/pT peaks
remove_artifacts: True

# Method to use for removing artifact peaks
remove_artifacts_method:  'blacklist' # options: 'blacklist', 'poly_a_t'

# Blacklist bed file
blacklist_file: refs/mm10_noise_blacklist_expand.bed

# Path for text file containing barcode whitelist
whitelist: refs/visium-v1.txt

# Path for text file containing spatial row/column indices of valid barcodes
spot_coords: refs/visium-v1_coordinates.txt

#######################################
# Configuration options for debug run #
#######################################

window_length: 70

poly_a_t_threshold: 20

# This needs to be specified if remove_artifacts is set!
genome_fasta: path/to/genome/fasta