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willtownes / quminorm-paper

supporting code for the quasi-UMIs single-cell RNA-seq paper
GNU Lesser General Public License v3.0
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Missing file in the preprocessing of grun_2016 data #3

Open zuoyi93 opened 3 years ago

zuoyi93 commented 3 years ago

Dear Dr. Townes,

Thanks for sharing this amazing repository and it really helps understand your paper!

However, I couldn't find the SraRunInfo.csv at the following location. It's not derived from the previous step, I believe. Would you please let me know where to get this file?

https://github.com/willtownes/quminorm-paper/blob/c726ca77b13612ca415bab30924568d27a8ef06e/real/grun_2016/01_data_loading.Rmd#L110

Thanks in advance!

Yi

willtownes commented 3 years ago

Thanks for your interest! Sorry I should have made it more clear in the Rmd. But as a quick solution, that is a CSV file you have to manually export from the sequence read archive (SRA). Here's how:

  1. Go go the GEO page for the dataset and scroll down to the relations section. There is a link to SRA with the identifier SRP074299.
  2. On the SRA page it will show a list of all the run files (these can be expanded into FASTQ later), in the top right there is a send to file menu (see screenshot). You want to export in the "Run Info" format. Save that file to the extdata subfolder and then you should be all set.

Screen Shot 2021-06-22 at 11 03 12 AM

willtownes commented 3 years ago

If you figure out a way to get this file in an automated fashion (eg with wget), please post here so we can all learn! It's annoying to have to do it manually for each dataset.

zuoyi93 commented 3 years ago

Dear Dr. Townes,

Thanks for your prompt reply! I was able to download it as per your instructions.

I'll leave this issue open to see if others have an automated way of getting this file.

Thanks again!

Yi