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allyhawkins avatar allyhawkins commented on June 15, 2024

After our discussion today in the ST benchmarking meeting, we have decided to use Spaceranger and provide the outputs from Spaceranger as a zip file. We should include the unfiltered and filtered output from Spaceranger, the web summary (equivalent to our qc report), the spatial folder, and a metadata file that we would add in with version information. This is approximately what the contents of the download for each library would then look like for the ST libraries.

├── SCPCL000000_filtered_files
│   ├── barcodes.tsv.gz
│   ├── features.tsv.gz
│   └── matrix.mtx.gz
├── SCPCL000000_spaceranger_summary.html
├── SCPCL000000_spatial
│   ├── aligned_fiducials.jpg
│   ├── detected_tissue_image.jpg
│   ├── scalefactors_json.json
│   ├── tissue_hires_image.png
│   ├── tissue_lowres_image.png
│   └── tissue_positions_list.csv
├── SCPCL000000_unfiltered_files
│   ├── barcodes.tsv.gz
│   ├── features.tsv.gz
│   └── matrix.mtx.gz
└── SCPCL00000_metadata.json

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jashapiro avatar jashapiro commented on June 15, 2024

I'm wondering if we might want to more directly mirror the Space Ranger outs directory, which might look more like this (basically package everything up within a folder for each library):

SCPCL000000
├── filtered_feature_bc_matrix
│   ├── barcodes.tsv.gz
│   ├── features.tsv.gz
│   └── matrix.mtx.gz
├── raw_feature_bc_matrix
│   ├── barcodes.tsv.gz
│   ├── features.tsv.gz
│   └── matrix.mtx.gz
├── spatial
│   ├── aligned_fiducials.jpg
│   ├── detected_tissue_image.jpg
│   ├── scalefactors_json.json
│   ├── tissue_hires_image.png
│   ├── tissue_lowres_image.png
│   └── tissue_positions_list.csv
├── SCPCL000000_metadata.json
└── SCPCL00000_spaceranger_summary.html

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allyhawkins avatar allyhawkins commented on June 15, 2024

This makes sense to me, I'm good with this organization.

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