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anlebreton / Scripts_from_Zeng_Lebreton_et_al._2023

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Mapping NCBI SRA IDs to metadata #1

Closed fantin-mesny closed 11 months ago

fantin-mesny commented 11 months ago

Good morning,

I am willing to re-analyze some data from your publication. I could download the reads from NCBI SRA, but cannot find in the publication which sample corresponds to OS or OM soil layers. I found here the file metatranscriptomique/0_metadata/metadata_all.txt, but it does not provide the same IDs as the SRA metadata. Could you please let me know how I can link the SRA IDs (Abies-x/Picea-x/Quercus-x, with x between 1 and 24) to the IDs in this table, or simply to soil layers OS/OM?

Many thanks, and best wishes, Fantin Mesny

anlebreton commented 11 months ago

Hi Fantin,

Can you provide me the metadata you got from SRA ? I can see the information you're looking for in the files names.

screenshot

Best, Annie

fantin-mesny commented 11 months ago

Hi Annie,

Thanks! Suprising that they appear in search results. I batch downloaded metadata associated to SRA runs of the bioproject. And these names are not in that table (see attached: SraRunTable.txt).

Anyways, I can manage with search results, I guess.

Thanks again, Fantin

anlebreton commented 11 months ago

Hi Fantin,

I added a new column on the file metatranscriptomique/0_metadata/metadata_all.tsv with the run number so you can merge these two metadata files.

Best, Annie