ARC minimal Example RNASeq
This is a minimal Example ARC packaging an mRNA-Seq dataset with metadata and computations.
Data origin
- see ./isa.investigation.xlsx for details.
- Published under: https://doi.org/10.1104/pp.15.01076
Setting up the arc structure using arcCommander
# initialize the structure
arc init
# set up investigation
arc i create --identifier samplearc_rnaseq
# add study folders to place input material and data
arc study add -s TalinumFacultativeCAM
arc study add -s TalinumGenomeDraft
# add assay folder to place assay data
arc assay add -s TalinumFacultativeCAM -a Talinum_RNASeq_minimalDescribe experiments using SWATE
| File | Selected swate template |
|---|---|
| studies/TalinumFacultativeCAM/isa.study.xlsx | "Plant growth" v. 1.1.2 |
| assays/Talinum_RNASeq_minimal/isa.assay.xlsx | "RNA extraction" v. 1.1.6 "RNA-Seq Assay" v. 1.1.7 |
Additional payload
The following folders are not part of the pure ARC
for details, see: ARC specs:Additional paylod
| Directory | Purpose |
|---|---|
| _GEO_submission | Example metadata files as required for submission to GEO |