RNA-seq Differential Expression, Alternative Splicing, Transcript Assembly and Gene Fusion

最新推荐文章于 2023-12-26 23:40:48 发布

Al_Liz_Well

最新推荐文章于 2023-12-26 23:40:48 发布

阅读量919

点赞数

分类专栏： RNA-seq 文章标签： RNA-seq Differential Alternative Splicing Transcript Assembly Gene Fusion

本文链接：https://blog.csdn.net/Al_Liz_Well/article/details/51721339

版权

本文介绍了RNA-seq数据分析的关键方面，包括如何评估差异表达，如通过估计变异性来计算p值；探讨了读取分布的泊松分布和负二项分布模型；并提到了一些常用的差异表达分析工具，如Cufflinks、LIMMA-VOOM和DESeq2。此外，还讨论了RPKM、FPKM和TPM等表达指数的优缺点。RNA-seq的剪接变异分析中，MATS工具用于多变量分析，而Tophat则用于分配reads到剪接异构体。在转录组装部分，介绍了参考依赖性和de novo组装方法。最后，简述了在癌症样本中常见的基因融合现象及其检测的挑战。

摘要由CSDN通过智能技术生成

RNA-seq Differential Expression:

Gene X’s expression in condition A doubles expression in condition B. But how reliable is this? What’s the chance of observing it by rendom? All comes to variation estimation! How to meassure the variance between different biological replicates. Once you have the variation estimation, you’re able to assign a p-value for expression changes. Variation can be estimated if you have many biological replicates.But in practice, we only have 2-3 replicates. What we can do next is proper statistical models.

Sequencing Read Distribution:

1. Poisson distribution:λ=E(X)=Var(X)

The easiest model for RNA-seq reads count is Poisson distribution.

Assumption : Mean = Variance

But: sequencing data is over-dispersed,not only RNA-seq (Mean<Variance)

2. Negative binomial: X ~ NB(r;p)( 2 parameters : r,p)

Definition : number of successe