figaro软件 dada2切断位置的确定 trimmomatic预处理

官网指导与学习

需要长度一样的配对双端 所以需要trimmomatic 预处理

下载与安装，下载用本地虚拟机就可以

git clone https://github.com/Zymo-Research/figaro.git
cd figaro
# depending on your system configuration, the following commands
# are either python3/pip3 or python/pip
python3 setup.py bdist_wheel
pip3 install --force-reinstall dist/*.whl
figaro -i /path/to/fastq/directory -o /path/to/output/files -a [amplicon length] \-f [forward primer length] -r [reverse primer length]

trimmomatic 预处理

一个细节

#导出的顺序
mySampleFiltered_1P.fq.gz - for paired forward reads
mySampleFiltered_1U.fq.gz - for unpaired forward reads
mySampleFiltered_2P.fq.gz - for paired reverse reads
mySampleFiltered_2U.fq.gz - for unpaired reverse reads

【CROP为保留长度】

trimmomatic PE -phred33 /home/dengqr/dataset/cheng/00sequences/Control100A_1.fq.gz /home/dengqr/dataset/cheng/00sequences/Control100A_2.fq.gz 1_16s_R1.fastq.gz 01fq.gz 1_16s_R2.fastq.gz 01fq.gz  HEADCROP:1 CROP:260 MINLEN:260trimmomatic PE -phred33 /home/dengqr/dataset/cheng/00sequences/Control102A_1.fq.gz /home/dengqr/dataset/cheng/00sequences/Control102A_2.fq.gz 2_16s_R1.fastq.gz 01fq.gz 2_16s_R2.fastq.gz 01fq.gz  HEADCROP:1 CROP:260 MINLEN:260trimmomatic PE -phred33 /home/dengqr/dataset/cheng/00sequences/Control101A_1.fq.gz /home/dengqr/dataset/cheng/00sequences/Control101A_2.fq.gz 3_16s_R1.fastq.gz 01fq.gz 3_16s_R2.fastq.gz 01fq.gz  HEADCROP:1 CROP:260 MINLEN:260trimmomatic PE -phred33 /home/dengqr/dataset/cheng/00sequences/Control109A_1.fq.gz /home/dengqr/dataset/cheng/00sequences/Control109A_2.fq.gz 4_16s_R1.fastq.gz 01fq.gz 4_16s_R2.fastq.gz 01fq.gz  HEADCROP:1 CROP:260 MINLEN:260

配对双端转到单独文件夹，并解压

需要考虑的问题 Attention

341F (5’-ACTCCTACGGGAGGCAGCAG-3’) and

806R (5’-GGACTACHVGGGTWTCTAAT-3’).

806-341=465

Amplicon size should only be the length of the targets sequence and should not include primers

465-20-20=425

可以多个样本一起处理的，记得解压在一起

fastq的命令方式一定要参照我的

figaro -i 1/ -o data1 -a 425 -f 1 -r 1
figaro -i 2/ -o data2 -a 425 -f 1 -r 1