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waldronlab / curatedMetagenomicDataCuration

Sample Metadata Curation for curatedMetagenomicData
https://waldronlab.io/curatedMetagenomicDataCuration/
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NCBI_accession corresponds to sample_id in place of run_id for HMP samples #16

Closed schifferl closed 6 years ago

schifferl commented 6 years ago

From @fplaza on December 6, 2017 14:51

Hello,

In the file _combinedmetadata.rda, the field NCBI_accession corresponds to the sample_id in place of the run_id for HMP samples.

For example: dataset_name | sampleID | subjectID | NCBI_accession HMP_2012 | SRS056519 | HMP_2012_765094712 | SRS056519 HMP_2012 | SRS018427 | HMP_2012_160218816 | SRS018427

Should be replaced by: dataset_name | sampleID | subjectID | NCBI_accession HMP_2012 | SRS056519 | HMP_2012_765094712 | SRR063503;SRR063504 HMP_2012 | SRS018427 | HMP_2012_160218816 | SRR059916;SRR059917

Thank you.

Copied from original issue: waldronlab/curatedMetagenomicData#115

schifferl commented 6 years ago

Thank you @fplaza. This applies to all of the HMP metadata?

schifferl commented 6 years ago

From @edoardopasolli on December 6, 2017 15:37

Thanks for catching this typo. I see that a similar problem is also affecting the KarlssonFH_2013 and the YuJ_2015 datasets.

@paolinomanghi could you generate the right NCBI_accession for these three datasets?

schifferl commented 6 years ago

From @fplaza on December 6, 2017 15:57

@schifferl Yes, all the HMP samples are concerned.

edoardopasolli commented 6 years ago

The issue has been fixed