YXF-测序仪和质量控制
2017-11-19 本文已影响14人
大宝贝喜欢徐先生
- 目前常用的测序仪
Illumina: high-throughput sequenching
IonTorrent: clinical application
PacBio Sequel: long read sequencing
MinION: portable, miniaturized device, robust and reliable
原理暂时没有搞明白 - 质量控制步骤--Quality control of data
质量控制：通过删去一些错误的数据来提高数据质量
质量控制步骤：Keep reads with an average quality over a threshold
Trim back the ends of reads until the measurements are reliable
Remove known synthetic sequences
质量控制工具：Trimomatic, cutadapt,bbduk - FastQC的结果解读--Visualizing data quality
FastQC is FASTQ quality visualization tool
length histogram: how many sequences of each length the data contains
quality histogram: 横轴是质量分数，纵轴是质量读数 - 使用multiQC聚合fastqc的输出结果
multiQC: Generate outputs that summarze multiple individual results.
安装：source activate bioinfo
conda install multiqc -y
使用：Get and unpack the data
Run fastqc and make it keep the data directories
Run multiqc on the resulting directories
最后生成一个multiqc_report.html 的输出结果
