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Prepare/Load metadata into Gemma #1

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mbelmadani opened this issue Jan 25, 2018 · 1 comment
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Prepare/Load metadata into Gemma #1

mbelmadani opened this issue Jan 25, 2018 · 1 comment
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enhancement gemma Features/Bug related to Gemma integration

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@mbelmadani
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Addressing request from PavlidisLab/Gemma#20

For GEO datasets/expression experiments, we would like to obtain:

  • The GSExxxxx
  • Pipeline parameters (Assembly, software versions, etc)
  • Fastq header information
  • Alignment information (may not be straightforward with RSEM)

To start, let's produce a text file in a "METADATA" directory similar to the Data directory.

@mbelmadani mbelmadani added enhancement gemma Features/Bug related to Gemma integration labels Jul 9, 2018
@mbelmadani
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Files are generated/moved over to the $METADATA location when the GatherMetadataGSE task is executed resolving the request from PavlidisLab/Gemma#20 in terms of the RNA-Seq pipeline.

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Labels
enhancement gemma Features/Bug related to Gemma integration
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