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validation_checklist.md

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validation_checklist.md

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Validation workflow (checklist)

  1. check prefixes in folder Counts: tree Counts/
  2. check prefix in CountMatrix_genes_TPM.tsv file
  3. check prefixes in folder MultiQC_out: tree MultiQC_out/
  4. add PCA report: qcfastq --tool=PCA .
  5. for quality control, download:
    • MultiQC report scp fear@130.192.101.241:/home/fear/WORKS/Endothelion/Lines/hCMEC_D3/GSE138309/MultiQC_out/GSExxxxxxx_multiqc_report.html .
    • PCA report scp fear@130.192.101.241:/home/fear/WORKS/Endothelion/Lines/hCMEC_D3/GSE138309/PCA_out/GSExxxxxxx_CountMatrix_genes_TPM/* .
  6. download metadata again and manually edit the extra field using nano (set 0 to exclude a Run) metaharvest -x=1 -e GSExxxxxxx > GSExxxxxxx_meta.csv
  7. delete FASTQ files rm *.fastq.gz
  8. make the TAR GZ compressed archive from the parent directory tar -czvf ./GSExxxxxxx/GSExxxxxxx.tar.gz GSExxxxxxx
  9. locally download files to upload to Zenodo later scp fear@130.192.101.241:/home/fear/WORKS/Endothelion/Lines/hCMEC_D3/GSExxxxxxx/GSExxxxxxx* .