Analysis of human T-cell RNA-seq

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DATA DOWNLOAD, QC, MAPPING AND READ COUNTING

To replicate the whole analysis, download the human GTF and FASTA files from Ensembl .
Subset GTF file for chromosome X and extract to annotations/Homo_sapiens.GRCh38.chrX.gtf and save FASTA of chromosome X to annotations/Homo_sapiens.GRCh38.dna.chromosome.X.fa.

Samples: run the data_download_map.sh for sample download, mapping and generating per gene counts.

Requirements: curl, fastq-dump, seqkit, fastqc, STAR, featureCounts.

DIFFERENTIAL EXPRESSION ANALYSIS

Run the analysis.R script.

Requirements: data.table, magrittr, edgeR and ggplot2 packages.