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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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Where can I find the fastq files for adata_with_ercc_genecode_counts_for_gatk_with_metadata.h5ad? #46

Open TdzBAS opened 1 year ago

TdzBAS commented 1 year ago

Hi,

thanks for this organized repositiory!

I want to analyze the adta-object for FACS which includes ercc-sequences. This should be the following file:

(https://s3.console.aws.amazon.com/s3/object/czb-tabula-muris-senis?region=us-west-2&prefix=Data-to-reproduce-figures/mutation-analysis-objs/adata_with_ercc_genecode_counts_for_gatk_with_metadata.h5ad)

But in the metadata are no information about the fastq-files. So I cant get them from SRA. But I see that there is the folder:

s3://czb-tabula-muris-senis/Plate_seq/3_month/

But I cannot map the cell_ids from to the fastq-files? How do I get the corresponding fastq-files?

Best, Tolga

TdzBAS commented 1 year ago

Maybe I must use the file s3://czb-tabula-muris-senis/Metadata/tabula-muris-senis-facs-official-raw-objcell-metadatacleaned_ids__read1_read2.csv

and map the cell_ids from the anndata-obj to the cell_ids in the metadata and find the urls to fastq file in the aws bucket?

Am I understanding it right that the fastq-files for tabula muris senis is only in the aws bucket and there is no SRA?

Best, Tolga