先新建一個fastqc.sh，內(nèi)容fastqc 文件名 -o 目標文件夾

bash fastqc.sh

multiqc

MultiQC是一款批量查看QC結(jié)果的軟件，大大節(jié)省了我們打開多個QC結(jié)果文件的時間

conda install multiqc

multiqc --help

multiqc ./fastqc --pdf

fastqc報告，需要去接頭？

cutadapt有一個弊端，需要自己指定接頭文件。這個軟件可以去掉reads中的adapter，低質(zhì)量的reads以及過長過短的reads，還可以對reads中含有N的進行處理。（cutadapt-a AGATCGGAAGAG --quality-base 33 -m 10 -q 20 --discard-untrimmed -o trim_data1.fqdata1.fq > cutadpt.info），這里--discard-untrimmed是把reads中不含有adapter的reads去掉。

trimmomatic

官網(wǎng)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

由于是對microRNA的測序結(jié)果，我把MINLEN:36去掉了～

然后再fastqc看一下效果：

場面一度十分尷尬。。。

然后我發(fā)現(xiàn)是因為我沒有指定adaptor的路徑～哼～這么不智能～

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

這算正常了？

應該可以了