3. Fastp/Trim_galore

1. Download and install conda and other software

See tutorial: https://www.jianshu.com/p/a84cd44bac67

1.1 Conda installation

# image of Tsinghua university open-source website to download wget - chttps://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda2-latest-Linux-x86_64.sh

# Install bash Miniconda2- Latest-Linux-x86_64.sh # change the image source configuration conda config - add channels athttps://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free

conda config --add channelshttps://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge conda config --add channelshttps://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda conda config --set show_channel_urls yes

1.2 Create a small environment

Create a software installation environment called Ymy conda cret-n ymy Python =3 View the current Conda environment conda info -- envs Activate Conda’s RNA environment conda activate RNA Exit the small environment conda deactivate ymy

1.3 Software installation

Install Fastp
conda Install -c bioconda Fastp
Install trim_galore
conda install -y trim_galore

2. Fastp quality control:

2.1. Single two-terminal data processing:

fastp -i in.R1.fq.gz -I in.R2.fq.gz -o out.R1.fq.gz -O out.R2.fq.gz

2.2. Batch processing:

ls *_1.fastq | while read id; do "fastp -i $id -o ${id%_*}.1.fastp.fq -I ${id%_*}_2.fastq -O ${id%_*}_2.fastp.fq -h ${id%_*}.html "; done

2.3. Html&json format report

Filtering results:

3.Trim_galore Quality Control Process

3.1. Single two-terminal data processing:

trim_galore /... /in.R1.fastq /... / In.r2.fastQ-Q 25 --length 50-e 0.1 -- Stringency 5-o /... / -a adapter1 -a2 adapter2 --paired

3.2. Batch processing of double-ended data:

cat trim.sh #! /bin/bash Dir =/public/home/yuanmy/q1(be sure to use absolute path here) cat config |while read id do arr=${id} fq1=${arr[0]} fq2=${arr[1]} Nohup trim_galore-q 20 --phred33 --length 36-e 0.1 -- Stringency 3 -- Paired -o $dir $fq1 $fQ2 & done

3.3. Interpretation of results:

Generate three intermediate files:

The number of bases trimmed by TRIM Galore was smaller than that of fastp: