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elixir-europe / rdmkit

ELIXIR Data Management Toolkit - Find the answers to your research data management questions here.
https://rdmkit.elixir-europe.org
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Additional info for page: Epitranscriptome data #1098

Open daniwelter opened 1 year ago

daniwelter commented 1 year ago

I would like to request additional information for the Epitranscriptome data page at /epitranscriptome_data. The page should cover in a bit more detail the kind of metadata that should be stored with analysis output files, since intermediate data files are not routinely stored. If standard analysis metadata logs are provided by the tools being described, this should be explicitly stated.

lauportell commented 1 year ago

Answer from contributors of this pages:

I went through the problem. From my side, I don’t think we should add further information because the protocol to detect RNA editing events starts from a table of RNA variants and then it proceeds through several filtering steps in which no metadata are introduced. Low quality variants are simply discarded and what we think the best candidates are written in the output table.

I don’t think that intermediate files are useful, they are all subsets of the original table. So, the only metadata to save are at the beginning and they are related to the specific experiment, I mean the accession number of the RNAseq run, the main features of the input RNA (if polyA+ or total RNA ribo depleted, if reads are stranded or not), the origin of RNA (tissue, cell line, healthy or affected) and probably the lab producing the data.