RNAseq 教程 (1.6)

# 目录

1.Module 1 - Introduction to RNA sequencing

1. Installation
2. Reference Genomes
3. Annotations
4. Indexing
5. RNA-seq Data
6. Pre-Alignment QC

2.Module 2 - RNA-seq Alignment and Visualization

1. Adapter Trim
2. Alignment
3. IGV
4. Alignment Visualization
5. Alignment QC

3.Module 3 - Expression and Differential Expression

1. Expression
2. Differential Expression
3. DE Visualization
4. Kallisto for Reference-Free Abundance Estimation

4.Module 4 - Isoform Discovery and Alternative Expression

1. Reference Guided Transcript Assembly
2. de novo Transcript Assembly
3. Transcript Assembly Merge
4. Differential Splicing
5. Splicing Visualization

5.Module 5 - De novo transcript reconstruction

1. De novo RNA-Seq Assembly and Analysis Using Trinity

6.Module 6 - Functional Annotation of Transcripts

1. Functional Annotation of Assembled Transcripts Using Trinotate

# 1.6 Pre-Alignment QC

在对齐之前，你可以使用 FastQC 来确定你的数据质量:

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

还有一个视频教程

http://www.youtube.com/watch?v=bz93ReOv87Y

尝试在 fastq 文件上运行 FastQC:

fastqc *.fastq.gz

查看一下结果

HBR_Rep1_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1_fastqc.html

# 练习 4

作业：在前面的实践练习中下载的其他 fastq 文件中运行 FASTQC。

提示：请记住，将这些数据存储在一个名为 “practice” 的独立工作目录中。

在文件 hcc1395_normal_1.fastq 上运行 FASTQC。并通过检查输出来回答这些问题。

问题

How many total sequences are there? 331,958

What is the range (x - y) of read lengths observed? 151

What is the most common average sequence quality score? 41

What does the Adaptor Content warning tell us? 有一些证据表明，Illumina 接头在 reads 的 3' 端。这表明去除对于该数据来说可能是必须的。