czbiohub-sf/tabula-muris-senis

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

TdzBAS opened this issue · 1 comments

TdzBAS commented

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

Maybe I must use the file s3://czb-tabula-muris-senis/Metadata/tabula-muris-senis-facs-official-raw-obj__cell-metadata__cleaned_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