From 9b4dfc2597df139910ff04b54f91dd7f693ed264 Mon Sep 17 00:00:00 2001 From: Dominik <dominik.brilhaus@hhu.de> Date: Fri, 24 Mar 2023 10:09:20 +0100 Subject: [PATCH] move setup notes to wiki --- README.md | 37 ++----------------------------------- 1 file changed, 2 insertions(+), 35 deletions(-) diff --git a/README.md b/README.md index 737da47..a5bed2e 100644 --- a/README.md +++ b/README.md @@ -1,41 +1,8 @@ -# ARC minimal Example RNASeq +# ARC minimal example RNASeq -This is a minimal Example ARC packaging an mRNA-Seq dataset with metadata and computations. +This is a minimal example ARC packaging an mRNA-Seq dataset with metadata and computations. ## Data origin - see [./isa.investigation.xlsx](./isa.investigation.xlsx) for details. - Published under: <https://doi.org/10.1104/pp.15.01076> - -## Setting up the arc structure using arcCommander - -```bash -# 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_minimal -``` - -## Describe 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<br>"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](https://github.com/nfdi4plants/ARC-specification/blob/main/ARC%20specification.md#additional-payload) - -Directory |Â Purpose ----- | ---- -[_GEO_submission](./_GEO_submission) | Example metadata files as required for submission to GEO -- GitLab