Tool: SRA Run Collector Google Sheets Add-on: Looking for feedback!
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gravatar for bimlay2
4 weeks ago by
bimlay220
bimlay220 wrote:

I recently put together a simple Google App Script add-on for sheets that retrieves run information from SRA from a GSE, SRP, or PRJNA accession.

The git repository can be found here. All of the code can be found in the Code.gs file.

SRA provides its metadata in XML format, but if you want to create an experimental matrix from public data, you need tabular data. Moreover, going from a GSE accession to a table of run emtadata is non-trivial. This tool allows you to simply pull all run information for a given study with a click of a button.

I'm looking for feedback and future directions for the tool. I'm not bound to the Google App Script platform. I could easily make a web app with this code foundation. I figured a sheets add-on would be very accessible.

Here is an example of output from the script: https://drive.google.com/file/d/1c4_7xwMjuB2de4oJuzhvr2uuODze7UXy/view?usp=sharing

rna-seq tool • 157 views
ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by bimlay220
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In case you have not seen : sra-explorer : find SRA and FastQ download URLs in a couple of clicks

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by genomax70k

Yes, I've seen this tool. My inspiration for this project is that I wanted to know sample attributes and various other metadata fields for the associated runs.

The desired output of my tool is not necessarily run numbers alone, which are easy to get from sra-explorer. Rather, my tool collects run information and metadata for multiple studies at once.

I've also found that SRA Explorer does not find all studies because of the way it interfaces with Eutils. My method will always find associated sequencing runs. For example, try GSE48812 with SRA Explorer.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by bimlay220

The script requires some major permissions

Can you be more specific what that exactly means? No offense, but I would for sure not sudo (or similar) any code that comes from Github. Who knows what would happen ;-)

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by ATpoint21k

Permissions as in permissions from Google. The script uses a URL fetch method to get information from NCBI. Google will request permission to do this before you can run the script.

This is not a command line tool. There are no real client permissions involved.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by bimlay220
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