## global parameter
# chromosome size
genome_size =  /home/a-m/lzhang97/seq/BOWTIE2_INDEXES/hg38/hg38M.genome 
# bowtie2 genome index prefix
bowtie2_index = /home/a-m/lzhang97/seq/BOWTIE2_INDEXES/hg38/hg38M
# path to the wigToBigWig
wig2bigwig = /home/a-m/lzhang97/seq/software/wigToBigWig 
# path to the Norma script
norma = /home/a-m/lzhang97/seq/software/Norma.py 

## tool specific paramter
# parameters of bowtie2, only support generic parameters (parameters not sensitive to each sample) e.g. scoring parameters, number of thread etc.
bowtie_opt = -t -p 16
# parameters of Norma
norma_opt = -r 20000 -w 20000

## experiment
# exp name, final TSA-seq score will be named as exp_name.bw
exp_name = HCT_E_SON_PD1_hg38 
# a list of fastq file for pulldown
fastq_pulldown = test_pulldown_2.fastq test_pulldown_2.fastq
# name for pulldown bam file (no suffix, such as .bam)
label_pulldown = HCT_E_SON_pulldown
# a list of fastq file for input
fastq_input = test_input_1.fastq
# name for input bam file 
label_input =  HCT_E_SON_input

# output
output_folder = test
