chillwei / dms_ngs

NGS analysis and data visualization of DMS library

DMS_NGS

NGS analysis and data visualization of DMS library

Merge reads of pair ended data

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

Further data filtering based on v-find

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")