先新建一个fastqc.sh，内容fastqc 文件名 -o 目标文件夹
bash fastqc.sh
multiqc
MultiQC是一款批量查看QC结果的软件，大大节省了我们打开多个QC结果文件的时间
conda install multiqc
multiqc --help
multiqc ./fastqc --pdf
cutadapt有一个弊端，需要自己指定接头文件。这个软件可以去掉reads中的adapter，低质量的reads以及过长过短的reads，还可以对reads中含有N的进行处理。（cutadapt-a AGATCGGAAGAG --quality-base 33 -m 10 -q 20 --discard-untrimmed -o trim_data1.fqdata1.fq > cutadpt.info），这里--discard-untrimmed是把reads中不含有adapter的reads去掉。
trimmomatic
官网有例子：http://www.usadellab.org/cms/?page=trimmomatic
Paired End:
java -jar trimmomatic-0.35.jar PE -phred33 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
This will perform the following:
Remove adapters (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10)
Remove leading low quality or N bases (below quality 3) (LEADING:3)
Remove trailing low quality or N bases (below quality 3) (TRAILING:3)
Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15 (SLIDINGWINDOW:4:15)
Drop reads below the 36 bases long (MINLEN:36)
Single End:
java -jar trimmomatic-0.35.jar SE -phred33 input.fq.gz output.fq.gz ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
This will perform the same steps, using the single-ended adapter file
由于是对microRNA的测序结果，我把MINLEN:36去掉了～
然后再fastqc看一下效果：
然后我发现是因为我没有指定adaptor的路径～哼～这么不智能～
trimmomatic SE -phred33 ./SRR5593145.fastq.gz ./SRR5593145_trim.fastq.gz ILLUMIACLIP:./adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15
