Workflow works in two continguous parts. Run workflow.sh to quantify your transcripts using Salmon. Then the newly-generated counts file is the input to the workflow.py script which will filter genes so that only genes that have a minimum count of 10 from any 3 of 10 samples will be kept. Then the counts are normalized to the 75th percentile. Finally log2ratio is calculated and written to a file.
- Adjust config.sh file to your environment
- Ensure you have all the tools installed that are named in config.sh
- Ensure you have sample files in a directory that correspond to the sample names in fastq_gz_file_pairs.txt
bash workflow.sh
- Adjust config.py file to suit your environment
- Ensure you have all the python packages that are imported at the top of the workflow.py file
- If you need to recreate gene_conversion.json, then run the gene_conversion.py file
python workflow.py
MIT
Free Software, Hell Yeah!