ARC mininmal Example RNASeq

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 for details.

Additional payload

The following folders are not part of the ARC
for details, see: ARC specs:Additional paylod

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 adding the files to the ARC, track them via git lfs

   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 runs/run1/01_kallisto_index    

4. Commit

Bumping to ARC v1.1 (23.03.2022)

by arcCommander / shell

depends on arcCommander v3 or higher

arc a list

arc study unregister -s TalinumFacultativeCAM # unregister old study version
arc study add -s TalinumFacultativeCAM # add fresh
mv TalinumFacultativeCAM.study.xlsx studies/TalinumFacultativeCAM/old.study.xlsx # move old study metadata to new study

arc study add -s TalinumGenomeDraft # add draft genome as study
mv externals/Talinum.gm.CDS.nt.fa studies/TalinumGenomeDraft/resources # mv genome to resources
rm -r externals
rm inv.json

arc assay register -s TalinumFacultativeCAM -a Talinum_RNASeq_minimal # re-register assay 
arc update

mv assays/Talinum_RNASeq_minimal/protocols/01_plant_material.md studies/TalinumFacultativeCAM/protocols # move plant growth from assay to study

arc assay remove -s TalinumFacultativeCAM -a RNASeq_Kallisto_quant # add computational parts as assay 

note: soft assay

by hand

• move plant growth sheet isa.assay to isa.study
• remove computational RNASeq sheet from assays as it partly duplicates the (not yet CWLed) kallisto workflow

add placeholder sample descriptors

arc_root=$(pwd)
cd studies/TalinumFacultativeCAM/resources/
touch \
DB_097 \
DB_099 \
DB_103 \
DB_161 \
DB_163 \
DB_165
cd $arc_root

Make workflows a bit more representative and reproducible (24.03.2022)

generate a common arc_root pointer

echo "~/03DataPLANT_gitlab/samplearc_rnaseq/" > workflows/_arc_local_wd