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czbiohub-sf / tabula-muris-senis

Tabula Muris Senis
http://tabula-muris-senis.ds.czbiohub.org
BSD 3-Clause "New" or "Revised" License
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Help downloading data in other ways #16

Closed ShuilinLiao closed 3 years ago

ShuilinLiao commented 4 years ago

It's appreciate to be able to download the Tabula Muris Senis data from Amazon. However, registering an AWS account requires binding a credit card. For some reasons, I cannot obtain a valid credit card, which causes me failing register an AWS account. Is it convenient for you to provide other ways to download data? Thank you so much!

aopisco commented 4 years ago

@ShuilinLiao the processed data is available from figshare

Do you need raw fastq files?

ShuilinLiao commented 4 years ago

Thanks for your prompt and kindly response. I think the processed data is sufficient. The published paper studying ageing tissues in mouse through single cell transcriptomic (nature 2020) interested me very much and I think it is useful for me to learn the analyze of single-cell sequencing data. However, due to my poor understanding, I have some questions about the structure about the git repository. I think the scirpts in the directory "1_tabula_muris_senis" can reduce the figures 1-4 in the published article, but I can not find the input data mentioned in the scripts from figshare.
For example, in the script titled with "1_tabula_muris_senis/11_figure_1/tabula-muris-senis-droplet-processing.ipynb", 3 data "MACA_10x_1_3_30.csv" , "TM_droplet_metadata.csv" and "TM_droplet_mat.h5ad" were coded as input data, but I can not find them from figshare. Therefore I am wondering whether my understanding is wrong or there are oder bewteen some scripts, which generate the mentioned data. Would you help me solve the questiones? Best wishes for you and looking forward to your kind reply.

aopisco commented 3 years ago

@ShuilinLiao can you give me a bit more context on what you’re trying to do?

aopisco commented 3 years ago

Hi Benjamin,

unfortunately the size of the dataset is not manageable through the more conventional channels. Let me know if you need help navigating AWS.

Best, Angela

On Wed, Nov 25, 2020 at 12:15 PM Benjamin Stewart notifications@github.com wrote:

@ShuilinLiao https://github.com/ShuilinLiao the processed data is available from figshare https://figshare.com/articles/dataset/Tabula_Muris_Senis_Data_Objects/12654728

Do you need raw fastq files?

I am looking to download either raw fastq files or the BAM files. Inputting credit card details for amazon to register for one of these accounts is pretty unpalatable and may not work for some users. Navigating aws is not straightforward.

Is there any way you can make these data available through more classical channels - tabula muris has the raw data on SRA which is easily accessible for example.

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