RNA-seq (RNA Sequencing), also called Whole Transcriptome Shotgun Sequencing(WTSS), is a technology that uses the capabilities of NGS to reveal a snapshot of RNA presence and quantity from a genome at a given moment in time. (http://en.wikipedia.org/wiki/RNA-Seq)
RNA-seq으로 알 수 있는 것들
- Gene expression profile
- Alternative splicing
- SNV mutation in transcript
- Novel transcript
- Gene fusion with or without DNA change
Total RNA-seq 실험시 분류별 빈도
- mRNA: 60~70%
- small Non-coding RNA: 20%
- lncRNA: 10%
RNA-seq 분석 파이프라인을 Tuxedo protocol이라고도 한다. 양복점 방법.
Table of Contents
팁 #
- liver와 lung의 발현 비교 분석을 하려면 두 데이터를 섞어서 돌린 후, 결과를 reference로 liver와 lung을 각각 맞춰봐야 한다.
관련 도구 #
- ENCODE-DCC/rna-seq-pipeline: Align reads, generate signal tracks, and quantify genes and isoforms.
- BioJupies: 웹에서 RNA-seq 데이터 분석 후, 결과를 Jupyter 노트북으로 제공
- htsint: a Python library for sequencing pipelines that combines data through gene set generation BMC Bioinformatics
논문 #
- DREAMSeq: An Improved Method for Analyzing Differentially Expressed Genes in RNA-seq Data Frontiers in Genetics
- Cancer transcriptome profiling at the juncture of clinical translation Nature Reviews Genetics : Cancer RNA-seq 리뷰
- RNA sequencing: the teenage years Nature Reviews Genetics : 지난 10년과 신기술들 리뷰
- Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis Nature Communications
- Simulation-based comprehensive benchmarking of RNA-seq aligners Nature Methods
- Translating RNA sequencing into clinical diagnostics: opportunities and challenges Nature Review Genetics
- A survey of best practices for RNA-seq data analysis Genome Biology
- Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks Nature Protocols : TopHat과 Cufflinks를 이용한 RNA-seq 분석 방법
교육자료 #
관련정보 #
- Parametric analysis of RNA-seq expression data RNA-seq Blog : 새로운 Normalization 방법 제안
- The Epigenetic Insights of RNA-Seq RNA-Seq Blog : ncRNA의 중요성이 더 커지고 있음. 실제 임상에서 필요한 정보는 다른 것보다 RNA-seq일 것임. 잘 정립된 BI 분석 플랫폼이 없는 것이 문제
- Dumpster diving in RNA-sequencing to find the source of every last read : Reference와 매핑되지 않는 일부 read들이 발견되는 이유
- SHOULD YOU TRANSFORM RNA-SEQ DATA: LOG, VST, VOOM? : 정규화 방법 논의 log, VST, VOOM.
- Bioconductor's RNA-seq workflow in Jupyter notebook format
Incoming Links #
[Medical Scholarly Articles] About (MedicalScholarlyArticle 0) #
- Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
- VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis
- hppRNA-a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of numerous samples
[Codes] About (Code 1) #
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Related Books (Book 4) #
Related Products (Product 5) #
Related Articles (Article 6) #
- Cloud computing
- Coronavirus disease 2019
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- HIV
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- NGS
- Pipeline for Bioinformatics
- RNA
- Rep-seq
- SNV calling from NGS data
- Sequence assembly
- Tuxedo protocol
- scRNA-seq
Related Education Events (EducationEvent 7) #
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Related Medical Scholarly Articles (MedicalScholarlyArticle 9) #
- Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data
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- Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
- VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis
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