Commit e5fa60f3 authored by Martin Kuhl's avatar Martin Kuhl
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Update README.md

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# ARC mininmal Example RNASeq
# ARCHIVED
This is a minimal Example ARC packaging an mRNA-Seq dataset with metadata and computations.
## Data origin
- Partly published under: https://doi.org/10.1104/pp.15.01076
- see [./isa.investigation.xlsx](./isa.investigation.xlsx) for details.
## Additional payload
> The following folders are not part of the ARC
> for details, see: [ARC specs:Additional paylod](https://github.com/nfdi4plants/ARC-specification/blob/main/ARC%20specification.md#additional-payload)
Directory | Purpose
---- | ----
[_GEO_submission](./_GEO_submission) | Example metadata files as required for submission to GEO
## Notes and ToDos
### Experimental metadata in isa.assay.xlsx
- split GEO SWATE templates into four sheets
- 1SPL01_plants
- 2EXT01_RNA
- 3ASY01_RNASeq
- 4COM01_RNASeq
### Adding large raw data via git lfs
1. Before addind the files to the ARC, track them via `git lfs`
```
git lfs track "*.fastq.gz"
git lfs track "01_kallisto_index"
```
2. Move / add the large data files to the respective folders
3. Add them via `git add`
```
git add assays/Talinum_RNASeq_minimal/dataset/
git add runs/run1/01_kallisto_index
```
4. Commit
latest version of this ARC: https://git.nfdi4plants.org/brilator/samplearc_rnaseq
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