indelicato_2023

Skeletal muscle transcriptomics dissects the pathogenesis of Friedreich´s Ataxia (FRDA)

RNA sequencing data analysis of skeletal muscle biopsies from FRDA patients pre- and post-treatment with rhuEPO and from healthy controls. Raw sequencing data can be downloaded from GEO (GSE226646) and should be placed in data/FRDA_01_RAW. Alternatively, the the raw counts matrix can be downloaded for downstream analyses.

Conda environment for analyses:

conda env create -n frda-epo -f envs/frda-epo.yml
conda activate frda-epo

Preprocessing

FastQC of the raw data

qsub preprocessing/fastqc.sh

Poly-A and quality trimming

source preprocessing/trimming.sh

Run the nf-core/rnaseq pipeline (parameters and reference genome paths can be set in 'preprocessing/nf.config')

source preprocessing/preprocessing.sh

Run a check if paired samples are matched to the same donor with NGSCheckMate-1.0.0

source preprocessing/sample_check.sh

Analysis

Run the downstream analysis scripts

Rscript -e "rmarkdown::render('00_Preprocessing_Results.Rmd')"
Rscript -e "rmarkdown::render('01_Differential_Expression.Rmd')"
Rscript -e "rmarkdown::render('02_Pathway_Analysis.Rmd')"
Rscript -e "rmarkdown::render('03_Figures.Rmd')"

Results

After execution of the analysis scripts, generated figures and tables can be found in 'results'.