1. 基本命令 fastp -i in.R1.fq.gz -I in.R2.fq.gz # 单端测序# 双端测序fastp -i in.R1.fq.gz -I in.R2.fq.gz \ -o out.R1.fq.gz -O out.R2.fq.gz \ –detect_adapter_for_pe
注：
-a, –adapter_sequence the adapter for read1. For SE data, if not specified, the adapter will be auto-detected. For PE data, this is used if R1/R2 are found not overlapped. (string [=auto])
自动生成质控文件fastp.html和fastp.json，可以通过–html 和–json指定文件名字。
thread 默认为2，可以设定 -w, –thread ，最大为16
2.处理带UMI的fastq数据 fastp -i in.R1.fq.gz -I in.R2.fq.gz \ -o out.R1.fq.gz -O out.R2.fq.gz \ –umi \ –umi_loc per_read \ –umi_len 6 \ –umi_prefix UMI \ –umi_skip 4 \ –detect_adapter_for_pe
参数说明
–umi # enable umi
–umi_loc per_read # read1和read2都有UMI
–umi_len 6 # UMI序列长度
–umi_prefix UMI #UMI序列前缀
–umi_skip 4 # UMI序列后要切除的碱基数
adapter相关参数
-a, –adapter_sequence the adapter for read1. For SE data, if not specified, the adapter will be auto-detected. For PE data, this is used if R1/R2 are found not overlapped. (string [=auto])
–adapter_sequence_r2 the adapter for read2 (PE data only). This is used if R1/R2 are found not overlapped. If not specified, it will be the same as <adapter_sequence> (string [=auto])
–adapter_fasta specify a FASTA file to trim both read1 and read2 (if PE) by all the sequences in this FASTA file (string [=])
–detect_adapter_for_pe by default, the auto-detection for adapter is for SE data input only, turn on this option to enable it for PE data.
其他filter参数一般用default。
参考
质控软件fastp常用参数说明_sinat_32872729的博客-CSDN博客_fastp
https://github.com/OpenGene/fastp