RNA-Seq & Hyperspectral Pre-processing

Purpose

This script (i) adds fieldbook data to RNA-Seq and hyperspectral input files, (ii) combines RNA-Seq and hyperspectral data, and (iii) saves the joined RNA-Seq and hyperspectral CSV file to disk for each transcript.

Arguments

• -r, --rnaseq_csv

  • RNA-Seq input CSV file

• -s, --spectral_csv

  • Hyperspectral input CSV file

• -f, --fieldbook_csv

  • Fieldbook input CSV file

• -o, --out_dir

  • Output directory, default='2019_cotton_rnaseq_spectra'

Running the code

Run with input files

You will need to specify the path to each CSV file as such:

./rnaseq_spectral_pre_processing.py -r ./data/Cotton_TPM_TOP25.csv -s ./data/2019averagescans.csv -f ./data/Duke_Fieldbook_2019.csv

Run without input files

If input files are not specified, the code will automatically read the input files from the CyVerse Data Store using public links:

./rnaseq_spectral_pre_processing.py