To finish planning of H5AD epic, we need to test outputs from Alevin/Fry pipeline to understand the H5AD file structure and contrast it to existing specifications.
CellXGene has a very clear structure, defined in the specification but we need to verify that random experiments from the CellXGene database adhere to the structure.
b) Test 5-10 experiments from the CellXGene database to verify that they adhere to the specification. (https://cellxgene.cziscience.com/datasets) Write down used datasets in this section of the planning document.
To finish planning of H5AD epic, we need to test outputs from Alevin/Fry pipeline to understand the H5AD file structure and contrast it to existing specifications.
CellXGene has a very clear structure, defined in the specification but we need to verify that random experiments from the CellXGene database adhere to the structure.
The goal of this ticket is to:
a) Contrast the expected results from the convert_mtx_to_h5ad in nf_core (https://github.com/nf-core/scrnaseq/blob/2.4.0/bin/mtx_to_h5ad.py) with the cellXGene specification.
b) Test 5-10 experiments from the CellXGene database to verify that they adhere to the specification. (https://cellxgene.cziscience.com/datasets) Write down used datasets in this section of the planning document.