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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

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


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

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QuantSeq 3'mRNAseq data analysis

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