Project Completion QA Checklist: Single cell transcriptome analysis of human pancreas

[jychien]

Project UUID: cddab57b-6868-4be4-806f-395ed9dd635a Project Title: Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns. Project Short Name: Single cell transcriptome analysis of human pancreas Submission UUID: 5cd8b827-e4fa-4ffa-86f5-f0f8302baee9 Environment: Production

• [x] Process QA of bundles
• [x] Metadata tsv validation: Run metadatatsv_validator.py

[jychien]

Process QA found the following issue:

1. Project short name has spaces and ideally should be computer readable and not so long. Added to HumanCellAtlas/hca-data-wrangling/issues/350
2. Would be good to have 'sequencing_protocol.paired_end' information for Smart-Seq2 datasets. Have started conversation with Matrix Service in slack.

[jahilton]

validator results...

• analysis_file.file_core.format:matrix, results aren't real format
• analysis_process.type.text:analysis & analysis_protocol.type.text:analysis entered but not ontologized These are across-the-board issues and can't be AUDR'd

Others...

• dissociation_protocol.protocol_core.publication_doi & enrichment_protocol.protocol_core.publication_doi https://doi.org/10.1101/108043 does not match pattern
• donor_organism.developmentstage.ontology has issues with wrong ID & wrong format ('' instead of ':')
• library_preparation_protocol.input_nucleic_acid_molecule.ontology:OBI:0000869 entered but not library_preparation_protocol.input_nucleic_acid_molecule.ontology_label
• project.insdc_project_accessions:SRP075496 does not match pattern
• sequence_file.file_core.format:fastq.gz not in ['fastq'] These issues have been noted on https://github.com/HumanCellAtlas/hca-data-wrangling/issues/350