NGS analysis and data visualization of DMS library
use 'Fastp' tool for input and output. see link: https://github.com/OpenGene/fastp
fastp -i in.R1.fq.gz -I in.R2.fq.gz -o out.R1.fq.gz -O out.R2.fq.gz
run find-variant_QW.py in terminal
change variables in find-variant_QW.py line 113 - 115 : adatpor sequence for NGS and input file name. line 119: output as a .csv file, change the filename as needed
if __name__ == "__main__":
adapters = Adapters("GGCGCGGTGTTAAAT", "CATCATCACCATCACCAT" )
fq_1 = "smurfp_ngs_merge.fq.gz"
#fq_2 = "30-982598147/17L_R2_clean.fq.gz"
start = time.perf_counter()
find_variants(adapters, fq_1, save_path = "filtered_smurfp.csv")