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czbiohub-sf / tabula-muris

Code and annotations for the Tabula Muris single-cell transcriptomic dataset.
https://www.nature.com/articles/s41586-018-0590-4
BSD 3-Clause "New" or "Revised" License
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AWS fastq file metadata #230

Closed gouinK closed 4 years ago

gouinK commented 4 years ago

Hi all, thank you for providing this great dataset on AWS. I was wondering if there is a metadata or annotation file that describes each of the samples in the 'senis/10x/fastq/' folder? Thanks!

aopisco commented 4 years ago

hi @gouinK, are you referring to the data in Tabula Muris (this repo) or Tabula Muris Senis (https://github.com/czbiohub/tabula-muris-senis)?

gouinK commented 4 years ago

Yes the Tabula Muris Senis one

On Thu, Nov 12, 2020, 8:44 PM aopisco notifications@github.com wrote:

hi @gouinK https://github.com/gouinK, are you referring to the data in Tabula Muris (this repo) or Tabula Muris Senis ( https://github.com/czbiohub/tabula-muris-senis)?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/czbiohub/tabula-muris/issues/230#issuecomment-726504535, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIABFHH6KSIVISLF3PVLV73SPS2RXANCNFSM4TUBFBPQ .

aopisco commented 4 years ago

@gouinK the most complete metadata is the csv in here https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE149590 do you want to get the fastq files and rerun them through cellranger or other pipeline but get the correct metadata?

gouinK commented 4 years ago

Perfect, that looks like I can get the annotation from the prefix on the cell barcode, thanks so much! Yes I plan to process this with cellranger v4 so that I can compare some of your mammary gland data to my own generated data.