Comments (3)
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
from scpca-nf.
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
from scpca-nf.
This makes sense to me, I'm good with this organization.
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