training example/readme.md

In wyguo/ThreeDRNAseq: 3D RNA-seq App enables RNA-seq data analysis to be done only within 3 Days.

3D RNA-seq training materials

Survey | Example data | Transcript quantification | 3D RNA-seq | Publications

Survey

Thank you for taking the time to participate in the survey. Your input is greatly appreciated and will help us to improve the 3D RNA-seq App and training.

https://forms.gle/SjV4PXCTAtoDytHS7

3D RNA-seq example data

https://www.dropbox.com/s/8fsceneq8jlegwi/3D_RNAseq_example_data.zip?dl=0

Click “Download” and unzip, you will get three datasets:

• Galaxy_example_data: example data for transcript quantification using Galaxy
• Arabidopsis_cold: example data from a study of Arabidopsis
• Embryonic_mice: example data from a study of mice

Transcript quantification using Galaxy

• Galaxy Europe link: https://usegalaxy.eu/
• Shared example data on Galaxy Europe: https://usegalaxy.eu/u/wbguo/h/3d-rna-seq-data---southampton
• User manual: https://github.com/wyguo/ThreeDRNAseq/tree/master/vignettes/user_manuals

• Video tutorial: https://www.youtube.com/watch?v=rqeXECX1-T4

• Or download example data from: https://www.dropbox.com/s/8fsceneq8jlegwi/3D_RNAseq_example_data.zip?dl=0

3D RNA-seq analysis

• 3D RNA-seq App link: https://ics.hutton.ac.uk/3drnaseq
• 3D RNA-seq App Github page: https://github.com/wyguo/ThreeDRNAseq
• 3D RNA-seq App user manual: https://github.com/wyguo/ThreeDRNAseq/tree/master/vignettes/user_manuals
• 3D RNA-seq App YouTube video: https://www.youtube.com/watch?v=rqeXECX1-T4

To see a demo video, click the screenshot

Alternative link on Bilibili: https://www.bilibili.com/video/BV1mS4y1g7uB/

R scripts to generate gene-transcript association table

library(rtracklayer)
file2read <- 'genomic.gtf' # mouse gtf
gtf <- import(file2read)
exon <- gtf[gtf$type=='exon']

mapping <- data.frame(TXNAME=exon$transcript_id,GENEID=exon$gene_id)
mapping <- unique(mapping)
write.csv(mapping,file='mapping.csv',row.names = F)

3D RNA-seq App publications:

• Guo W, Tzioutziou NA, Stephen G, Milne I, Calixto CPG, Waugh R, et al. 3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists. RNA Biol. 2020;00:1–14.
• Calixto CPG, Guo W, James AB, Tzioutziou NA, Entizne JC, Panter PE, et al. Rapid and dynamic alternative splicing impacts the arabidopsis cold response transcriptome. Plant Cell. 2018;30:1424–44.
• Research used 3D RNA-seq App: https://scholar.google.com.au/scholar?oi=bibs&hl=en&cites=10705638438297153434

Reference transcritp dataset (RTD) publications:

• Coulter M, Entizne JC, Guo W, Bayer M, Wonneberger R, Milne L, et al. BaRTv2: A highly resolved barley reference transcriptome for accurate transcript‐specific RNA‐seq quantification. Plant J. 2022.
• Zhang R, Kuo R, Coulter M, Calixto CPG, Entizne JC, Guo W, et al. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biol 2022 231. 2022;23:1–37.
• Rapazote-Flores P, Bayer M, Milne L, Mayer CD, Fuller J, Guo W, et al. BaRTv1.0: An improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq. BMC Genomics. 2019;20.
• Zhang R, Calixto CPG, Marquez Y, Venhuizen P, Tzioutziou NA, Guo W, et al. A high-quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Nucleic Acids Res. 2017;45:5061–73.
• Zhang R, Calixto CPG, Tzioutziou NA, James AB, Simpson CG, Guo W, et al. AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana. New Phytol. 2015;208:96–101.

wyguo/ThreeDRNAseq documentation built on Feb. 12, 2024, 2:14 a.m.