config_hg38.yaml

#Snakemake configuration file

#project directory this ine needs to be changed
#proj_dir: /project2/xinhe/alan/downsampling_GBM/

#directory with additional scripts
scripts: /project2/xinhe/alan/dropseq_pipeline/Scripts/

#logfile
dir_log: log/
#Genome index for STAR aligner
genome_index: /project2/xinhe/alan/refGenome/STAR/

#transcript file
txn_file: /project2/xinhe/alan/refGenome/hg38_UCSC/gencode.v27.w.introns.gtf

#expected number of cells the value is the upper bound, at least 10% of this value will be lower bound so make sure to adjust it
cell_num: 3000

#downsampling
downsample: ["1"]

# which feature to count on
type: ["exon","intron"]

# cell barcode UMI Configuration
barcode: "CCCCCCCCCCCCNNNNNNNN"