-
Notifications
You must be signed in to change notification settings - Fork 349
Description
I use fastp (version 0.24.1) to clean wgbs library fastq data and find that read1 still retains many adapter. The command follows as
fastp --detect_adapter_for_pe -w 8 -i /mnt/NexData_file/home/zsr/1.develop/1.WGBS/1.FASTQ/CW619_1.fastq.gz -I /mnt/NexData_file/home/zsr/1.develop/1.WGBS/1.FASTQ/CW619_2.fastq.gz -o results/01.data_clean/cleandata/CW619_1.clean.fastq.gz -O results/01.data_clean/cleandata/CW619_2.clean.fastq.gz --unpaired1 results/01.data_clean/fastp/CW619_u.clean.fastq.gz --unpaired2 results/01.data_clean/fastp/CW619_u.clean.fastq.gz -5 --cut_front_window_size 4 --cut_front_mean_quality 20 -3 --cut_tail_window_size 4 --cut_tail_mean_quality 20 --cut_right --cut_right_window_size 4 --cut_right_mean_quality 20 -q 15 -u 40 -e 20 -l 30 -p -P 20 -j results/01.data_clean/fastp/CW619_fastp.json -h results/01.data_clean/fastp/CW619_fastp.html
The read 1 clean datas include many adapter like