RNAseq 教程 (5)

# 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

# 5. De novo RNA-Seq Assembly and Analysis Using Trinity

任务

• Generating a Trinity de novo RNA-Seq assembly

• Evaluating the quality of the assembly

• Quantifying transcript expression levels

• Identifying differentially expressed (DE) transcripts

• Functionally annotating transcripts using Trinotate and predicting coding regions using TransDecoder

• Examining functional enrichments for DE transcripts using GOseq

• Interactively Exploring annotations and expression data via TrinotateWeb

# 数据内容

在本课程中，将使用本文的数据：通过 RNA-Seq 定义光滑念珠菌的转录组特征 Linde et al. Nucleic Acids Res. 2015 WT 以及 GSNO 的数据。

vi SRR_Acc_List.txt

SRR1582646

SRR1582647

SRR1582648

SRR1582649

SRR1582650

SRR1582651

prefetch --option-file Seqs/SRR_ACC_Lists.txt ./

vi sh.sh

cat SRR_Acc_List.txt |while read i

do

fastq-dump --defline-seq '@$sn[_$rn]/$ri' --split-files -A $i ${i}/${i}.sra

done

sh sh.sh

下载结束后给所有文件重命名

GSNO_SRR1582646_1.fastq

GSNO_SRR1582646_2.fastq

GSNO_SRR1582647_1.fastq

GSNO_SRR1582647_2.fastq

GSNO_SRR1582648_1.fastq

GSNO_SRR1582648_2.fastq

wt_SRR1582649_1.fastq

wt_SRR1582649_2.fastq

wt_SRR1582650_1.fastq

wt_SRR1582650_2.fastq

wt_SRR1582651_1.fastq

wt_SRR1582651_2.fastq