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Extracting the gene annotation table
Sam Minot edited this page Apr 4, 2022
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It can be difficult some times to load data from an HDF5 file. To help make this process a bit easier, we have made a small Python script that will read the gene annotation table from a geneshot results HDF5 file and save it as a CSV.
You can find the script here: https://gist.github.com/sminot/1294d4f93c3b4e45f1de56ab95d9a8ce
To use it, simply save the file as geneshot_extract_gene_annot.py
and then run:
geneshot_extract_gene_annot.py --input_fp RESULTS.hdf5
(where RESULTS.hdf5
is the *.results.hdf5 file produced in your geneshot output folder)
- Getting Started
- De novo vs. Reference-Based Analysis
- Running Geneshot
- Output Files
- Input File Format
- Nextflow Configuration
- Helpful Scripts:
- Concepts: