Tau Haplotype Neuron RNAseq Differential Analysis

Pipeline for differential RNA-seq analysis comparing H1H1 vs. H2H2 iPSC-derived neurons (Batch 1)

Pipeline Stages:

1. Prepocessing of the gene expression count matrix
   1. gene filtering by CPM and %samples
   2. CQN normalization code: 3_GeneExpr_Filtering_CQN_normalization.R
2. Build linear model
   1. correlation of biological and technical covariates with top PCs of the normalized gene expression matrix
   2. all VIF < 2.5 code: 4_PCA_Build_linear_model.R
3. Differential analysis
   1. DESeq2 code: 5_DEseq2.R

File Locations

• data_provided/ contains the raw gene count matrix, gene effective length, picard metrics, and metadata.
• code/ contains all the scripts.
• results/ contains some of the results from running the scripts.