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

Made by Kicheol Kim (January 28. 2019. updated)