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10x data SRA without technical UMI or Cellbarcode reads #257

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emiliosk opened this issue Oct 10, 2024 · 0 comments
Open

10x data SRA without technical UMI or Cellbarcode reads #257

emiliosk opened this issue Oct 10, 2024 · 0 comments

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@emiliosk
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Hi!

I've been wanting to download the raw counts from a few files through SRA using for example:
prefetch SRR6835854

Unfortunately now the reads in SRA are not paired to the UMIs and the cell barcode, so it would be impossible to trace back in case of aligning again.

Would you know how I can get data with the data with the technical reads as well?

I see sometimes In the issues commenting on sharing the data through AWS (through this link for example: https://s3.console.aws.amazon.com/s3/buckets/czb-tabula-muris-senis?region=us-west-2&tab=objects
However I have no profile and amazon doesn't allow me to create a profile, if I go through the sign up link.

I see still in SRA I could download a bam file through a free egress link; for example in this sample:
https://sra-pub-src-1.s3.amazonaws.com/SRR6835854/10X_P7_2.bam.1

however I wonder if the data for AWS is including rather fastq files, instead of bam files for the 10x data!

But mainly, my question is if there are fastq files I could get that have both technical reads and biological read?

Thank you so much!

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