kneaddata的下载,安装,使用:
宏转录组分析:kneaddata质控、SortMeRNA去rRNA
1 FastQC
主页:
下载页:
http://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc
下载,安装:
wget -c http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip
unzip fastqc_v0.11.9.zip
cd FastQC
chmod 755 fastqc
fastqc --help
使用:
mkdir fastqc
/hwfssz1/ST_META/PN/hutongyuan/software/FastQC/./fastqc SRR413773_1.fastq -o fastqc/
/hwfssz1/ST_META/PN/hutongyuan/software/FastQC/./fastqc SRR413773_2.fastq -o fastqc/
2 Trimmomatic
主页,下载页:
下载,安装:
wget -c http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.39.zip
cd Trimmomatic-0.39
java -jar trimmomatic-0.39.jar --help
conda install kneaddata # 自动安装trimmomatic
conda activate env
trimmomatic --help
使用:
time trimmomatic PE -phred33 -threads 40 \
SRR1778451_1.fastq SRR1778451_2.fastq \
trimmomatic/SRR1778451_1_paired.fastq \
trimmomatic/SRR1778451_1_unpaired.fastq \
trimmomatic/SRR1778451_2_paired.fastq \
trimmomatic/SRR1778451_2_unpaired.fastq \
SLIDINGWINDOW:4:20 MINLEN:50
3 Bowtie2
下载,安装:
conda install bowtie2
建库:
bowtie2-build -f hg38.fasta hg38 --threads 16
比对-单端:去宿主,取unmapped序列 速度极慢,不知为何?
mkdir bowtie2
bowtie2 -f -U SRR413773_1.fasta \
-p 16 --quiet \
-S bowtie2/SRR413773_1.sam \
-x temple/TF01-11 \
--al bowtie2/SRR413773_1.tsv
rm bowtie2/SRR413773_1.sam
比对-双端:去宿主,取unmapped序列
time bowtie2 -q -p 40 --quiet \
-1 trimmomatic/SRR1778451_1_paired.fastq \
-2 trimmomatic/SRR1778451_2_paired.fastq \
-S bowtie2/SRR1778451.sam \
-x /public/home/zzumgg03/huty/databases/hg38/hg38 \
--un-conc bowtie2/SRR1778451_bowtie2.fastq
rm bowtie2/SRR1778451.sam
参数:
-q: fastq [标签]
-f: fasta [标签]
--phred33: 测序碱基的质量体系,现在基本都是33
-p: 线程数
--no-unal:不保留未必对上的记录
-U: unpaired
-1/-2: paired read1 read2
-x: temple
-S: output sam
--al: unpaired aligned
--un: unpaired unaligned
--al-conc: paired aligned
--un-conc: paired unaligned
4 kneaddata
下载,安装:默认同时安装trimmomatic bowtie2 fastqc
conda install kneaddata
kneaddata --help
质检,修剪,去宿主:
source /public/home/zzumgg03/huty/softwares/miniconda3/etc/profile.d/conda.sh
conda activate r403
time kneaddata -t 40 -v \
-i rawdata/SRR_list_8/SRR1778450/SRR1778450_1.fastq \
-i rawdata/SRR_list_8/SRR1778450/SRR1778450_2.fastq \
-o result/kneaddata/SRR_list_8/ \
--trimmomatic ~/huty/softwares/miniconda3/envs/r403/share/trimmomatic-0.39-1/ \
--max-memory 80g \
--trimmomatic-options "SLIDINGWINDOW:4:20 MINLEN:50" \
-db /public/home/zzumgg03/huty/databases/hg38/ \
--bowtie2-options "--very-sensitive --dovetail --reoeder" \
--fastqc ~/huty/softwares/miniconda3/envs/r403/bin/ \
--run-fastqc-start \
--run-fastqc-end \
--remove-intermediate-output
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