Process Ovary RNA-Seq data

The main script is IVF_data_processing.sh. This runs the whole pipeline at once on the 15 samples. However, it is recommended to run the run-scripts separately, assess the QC reports along the way and adjust accordingly.

1. Clone the respository

git clone https://github.com/melparker101/Ovary-IVF-data

cd Ovary-IVF-data

2. Download reference genome files

# Make a directory for the reference genome
mkdir ref

# Alternatively, download gencode files (this is recommended in the STAR manual)
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_42/GRCh38.primary_assembly.genome.fa.gz -P ref
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_42/gencode.v42.primary_assembly.annotation.gtf.gz -P ref

# Decompress files
# Gunzip invokes gzip -d
for f in ref/*.gz ; do gunzip -c "$f" > "${f%.*}" ; done

# Alternatively, download ensembl files
wget https://ftp.ensembl.org/pub/release-108/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
wget https://ftp.ensembl.org/pub/release-108/gtf/homo_sapiens/Homo_sapiens.GRCh38.108.gtf.gz

GMT files can be downloaded from: https://wikipathways-data.wmcloud.org/current/gmt/