> For the complete documentation index, see [llms.txt](https://ycl6.gitbook.io/rna-seq-data-analysis/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://ycl6.gitbook.io/rna-seq-data-analysis/rna-seq_analysis_workflow.md).

# RNA-Seq Analysis Workflow

Below shows a general workflow for carrying out a RNA-Seq experiment. In this guide, I will focus on the pre-processing of NGS raw reads, mapping, quantification and identification of differentially expressed genes and transcripts.

![Workflow](https://2175465529-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-M44VuvT-GOxd2-xMygM%2F-M44Vv9Erqxz_QwrCvEL%2F-M44VywoGv5YGTiBOS2b%2FWorkflow.png?generation=1586009218649085\&alt=media)