一、安装java环境
已经安装好了
二、fastqc安装
cd ~/Biosofts #进入目录
wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.7.zip #通过链接下载
mkdir ~/Biosofts/fastqc #创建文件夹
unzip /disk1/shares/fastqc_v0.11.7.zip -d ~/Biosofts/ #解压
chmod +x ~/Biosofts/FastQC/fastqc #chmod +x就是赋予用户文件的执行权限
~/Biosofts/FastQC/fastqc -h #查看
echo 'export PATH=~/Biosofts/FastQC:$PATH'>>~/.bashrc #加入环境变量
source ~/.bashrc #激活改变后的环境变量
fastqc -h #查看
三、fastqc评价测试数据质量
fastqc /disk1/shares/Seqs/Akle_TTAGGC_L004_R2_001.fastq.gz -o ~
查看
四、multiqc整合多个质控结果
conda create --name python2 python=2.7 -c
conda create --name python2 python=2.7 -c https://mirrors.ustc.edu.cn/anaconda/cloud/bioconda/ -y
结果出错,找不到,---原因可能是未启动conda
解决问题:
conda #查看conda
conda env list #查看conda的环境变量
conda activate python2 #激活python2
conda init bash
conda activate python2 #再次尝试激活
exit #重新进入服务器
conda activate python2 #再次激活python2
conda install multiqc -c https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
multiqc .
cd Biosofts #进入目录
ls #查看文件
(1).在服务器查看文件
less multiqc_report.html #查看文件内容
(2).在Windows查看
先拖拽下载到桌面上,再点击打开查看
二、安装seqtk
# sudo apt-get install seqtk
已经安装好了,不需要重新安装
gunzip -c /disk1/shares/Seqs/Akle_TTAGGC_L004_R1_001.fastq.gz |seqtk sample -s 60 - 500 >test500.fq
wc -l test500.fq
less test500.fq
三、Trimmomatic安装运行
# wget http://www.usadellab.org/cms/uplo ads/supplementary/Trimmomatic/Trimmomatic-0.38.zip
已经下载好了,不需要重复下载
unzip /disk1/shares/Trimmomatic-0.38.zip -d ~/Biosofts/
java -jar ~/Biosofts/Trimmomatic-0.38/trimmomatic-0.38.jar
运行结果:202031107010217@xiaoming-HP:~$ unzip /disk1/shares/Trimmomatic-0.38.zip -d ~/Biosofts/
Archive: /disk1/shares/Trimmomatic-0.38.zip
creating: /disk1/202031107010217/Biosofts/Trimmomatic-0.38/
inflating: /disk1/202031107010217/Biosofts/Trimmomatic-0.38/LICENSE
inflating: /disk1/202031107010217/Biosofts/Trimmomatic-0.38/trimmomatic-0.38.jar
creating: /disk1/202031107010217/Biosofts/Trimmomatic-0.38/adapters/
inflating: /disk1/202031107010217/Biosofts/Trimmomatic-0.38/adapters/NexteraPE-PE.fa
inflating: /disk1/202031107010217/Biosofts/Trimmomatic-0.38/adapters/TruSeq2-PE.fa
inflating: /disk1/202031107010217/Biosofts/Trimmomatic-0.38/adapters/TruSeq2-SE.fa
inflating: /disk1/202031107010217/Biosofts/Trimmomatic-0.38/adapters/TruSeq3-PE-2.fa
inflating: /disk1/202031107010217/Biosofts/Trimmomatic-0.38/adapters/TruSeq3-PE.fa
inflating: /disk1/202031107010217/Biosofts/Trimmomatic-0.38/adapters/TruSeq3-SE.fa
202031107010217@xiaoming-HP:~$ java -jar ~/Biosofts/Trimmomatic-0.38/trimmomatic-0.38.jar
Usage:
PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] [-validatePairs] [-basein <inputBase> | <inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...
or:
SE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog <trimLogFile>] [-summary <statsSummaryFile>] [-quiet] <inputFile> <outputFile> <trimmer1>...
or:
-version
202031107010217@xiaoming-HP:~$
java -jar ~/Biosofts/Trimmomatic-0.38/trimmomatic-0.38.jar PE -phred33 /disk/shares/Seqs/test_7942raw_1.fq.gz /disk/shares/Seqs/test_7942raw_2.fq.gz ./trim_out/output_forward_paired.fq.gz ./trim_out/output_forward_unpaired.fq.gz ./trim_out/output_reverse_paired.fq.gz ./trim_out/output_reverse_unpaired.fq.gz ILLUMINACLIP:/disk/teaching/Biosofts/Trimmomatic-0.38/adapters/TruSeq2-PE.fa:2:30:10 SLIDINGWINDOW:5:20 LEADING:20 TRAILING:20 MINLEN:75
java -jar ~/Biosofts/Trimmomatic-0.38/trimmomatic-0.38.jar
less ~/Biosofts/Trimmomatic-0.38/trimmomatic-0.38.jar #查看文件