https://github.com/baranzinilab/rnaseq_quantseq_fancy
QuantSeq 3'mRNAseq data analysis
https://github.com/baranzinilab/rnaseq_quantseq_fancy
Last synced: 5 months ago
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QuantSeq 3'mRNAseq data analysis
- Host: GitHub
- URL: https://github.com/baranzinilab/rnaseq_quantseq_fancy
- Owner: BaranziniLab
- License: gpl-3.0
- Created: 2019-01-29T03:49:09.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2019-01-29T17:22:21.000Z (about 7 years ago)
- Last Synced: 2025-02-27T21:49:08.866Z (about 1 year ago)
- Language: R
- Homepage:
- Size: 26.4 KB
- Stars: 0
- Watchers: 1
- Forks: 1
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# QuantSeq 3'mRNAseq data analysis
Code for RNA-Seq data analysis of the paper titled "Aberrant oligodendroglial-vascular interactions disrupt the Blood Brain Barrier triggering CNS inflammation" (Jianqin Niu, Hui-Hsin Tsai, Kimberly Hoi, Nanxin Huang, Guangdan Yu, Kicheol Kim, Sergio Baranzini, Lan Xiao, Jonah R. Chan, Stephen P.J. Fancy). (2019) Nature Neuroscience (Accepted)
The sequencing library was prepared according to the manufacturer's instructions (Lexogen).
## Analysis workflow
#### 1. Trim Galore v0.4.4 with CutAdapt v1.14: Trimming illumina adaptor
#### 2. FastQC v0.11.6: QC of fastq file
#### 3. STAR aligner v2.5.0a: sequence alignment
- genome reference: Gencode mouse genome reference (M14), https://www.gencodegenes.org/mouse/release_M14.html
#### 4. Statistical analysis using R and Bioconductor
- R version 3.5.1 (2018-07-02) and Bioconductor version 3.7 (BiocInstaller 1.30.0)
- Additional packages: ggplot2_3.1.0, RColorBrewer_1.1-2, pheatmap_1.0.10, DESeq2_1.20.0, readr_1.2.1
### References
- Martin M. (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17(1):10-12.
- Andrews S. (2017). FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc
- Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29(1):15-21.
- Krueger F. (2017) Trim Galore! Available online at: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore
- R Core Team (2018). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.
- Hadley Wickham, Jim Hester and Romain Francois (2018). readr: Read Rectangular Text Data. R package version 1.2.1. https://CRAN.R-project.org/package=readr
- Love, M.I., Huber, W., Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15(12):550 (2014)
- H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.
- Erich Neuwirth (2014). RColorBrewer: ColorBrewer Palettes. R package version 1.1-2. https://CRAN.R-project.org/package=RColorBrewer
- Raivo Kolde (2018). pheatmap: Pretty Heatmaps. R package version 1.0.10. https://CRAN.R-project.org/package=pheatmap
- Hadley Wickham, Jim Hester and Romain Francois (2018). readr: Read Rectangular Text Data. R package version 1.2.1. https://CRAN.R-project.org/package=readr
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Made by Kicheol Kim (January 28. 2019. updated)