重复序列元件定量分析

1引言

前面讲到了怎么下载重复元件的基因组位置及注释信息,这里再分享两款专门对重复元件进行定量的两款软件 TEtranscripts 和 SQuIRE。

2TEtranscripts

TEtranscripts 软件 2015 年发表在 Bioinformatics 期刊上:

摘要:

• Motivation: Most RNA-seq data analysis software packages are not designed to handle the complexities involved in properly apportioning short sequencing reads to highly repetitive regions of the genome. These regions are often occupied by transposable elements (TEs), which make up between 20 and 80% of eukaryotic genomes. They can contribute a substantial portion of transcriptomic and genomic sequence reads, but are typically ignored in most analyses.
• Results: Here, we present a method and software package for including both gene- and TE-associated ambiguously mapped reads in differential expression analysis. Our method shows improved recovery of TE transcripts over other published expression analysis methods, in both synthetic data and qPCR/NanoString-validated published datasets.

主要分析流程:

软件 github 地址:

https://github.com/mhammell-laboratory/TEtranscripts

具体使用方法可以去 github 查看安装和使用。

3SQuIRE

SQuIRE 软件于 2019 年发表在 Nucleic Acids Research 期刊上:

摘要:

Transposable elements (TEs) are interspersed repeat sequences that make up much of the human genome. Their expression has been implicated in development and disease. However, TE-derived RNA-seq reads are difficult to quantify. Past approaches have excluded these reads or aggregated RNA expression to subfamilies shared by similar TE copies, sacrificing quantitative accuracy or the genomic context necessary to understand the basis of TE transcription. As a result, the effects of TEs on gene expression and associated phenotypes are not well understood. Here, we present Software for Quantifying Interspersed Repeat Expression (SQuIRE), the first RNA-seq analysis pipeline that provides a quantitative and locus-specific picture of TE expression (https://github.com/wyang17/SQuIRE). SQuIRE is an accurate and user-friendly tool that can be used for a variety of species. We applied SQuIRE to RNA-seq from normal mouse tissues and a Drosophila model of amyotrophic lateral sclerosis. In both model organisms, we recapitulated previously reported TE subfamily expression levels and revealed locus-specific TE expression. We also identified differences in TE transcription patterns relating to transcript type, gene expression and RNA splicing that would be lost with other approaches using subfamily-level analyses. Altogether, our findings illustrate the importance of studying TE transcription with locus-level resolution.

主要分析流程:

软件 github 地址:

https://github.com/wyang17/SQuIRE

具体使用方法可以去 github 查看安装和使用。

4TEToolkit

TEtranscripts 包含在 TEToolkit里面的, 这个里面有好几个工具针对不同测序类型来对 转座元件 进行定量分析:

Software

最后,大家可根据自己需求对应选择合适好用的软件进行分析。

5结尾

路漫漫其修远兮,吾将上下而求索。

欢迎加入生信交流群。加我微信我也拉你进 微信群聊 老俊俊生信交流群 (微信交流群需收取 20 元入群费用,一旦交费,拒不退还!(防止骗子和便于管理)) 。QQ 群可免费加入, 记得进群按格式修改备注哦。