This file is an input file for Tapestri’s Mosaic Notebooks. Data produced by pipelines is stored in a structured HDF5 file. This file can contain data for one or more samples. Each sample, in turn, can contain data for one or more "assays", where each assay contains data for a different analyte. The .h5 file consist of the following details:
- Metadata like the run name, panel name, panel size, sequencing metrics, and ADO details.
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Assays – 1 assay for per analyte:
- DNA variant data which is the same data used to generate the .loom files and can be used for SNV-based analysis.
- DNA read count data consists of the barcode read distribution matrix that is used for analyzing copy number changes.
- Protein read count data consists of the protein reads distribution matrix used for phenotype analysis.
- RNA read count data consists of the RNA reads distribution matrix used for gene expression analysis.
- All barcode assay group is the read count information for all the barcodes and not just the barcodes called as cells.
For multisample Tapestri run there are multiple h5 files -
- <run-prefix>.h5 - One h5 file for the full multisample run
- <run-prefix>.<sample>.dmx.h5 - One h5 file for each sample with assays filtered to retain only cells from the sample. The following data in the sample h5 is updated:
- Row attributes in all assays
- Column attributes in all assays
- Data layer in all assays