Run RNAseq re-analysis

[KittyMurphy]

• [x] Trim adapter content
• [x] STAR alignment
• [x] Transcript quantification
• [x] Differential expression analysis
• [x] WGCNA

[KittyMurphy]

Previously, I ran the alignments with the RNA-seq and ATAC-seq data using two different reference genome files (both were hg38).

This time I've re-run the RNA-seq with the same genome file used for the ATAC-seq data, which has been recommended for use with NGS data and is discussed in this blog.

Alignment with STAR also requires a gtf file, here I've used gencode.v44.annotation.gtf as it is the most up to date and is also what the bioconductor transcript database TxDb.Hsapiens.UCSC.hg38.knownGene is based on.