Tutorial: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
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gravatar for CandiceChuDVM
4 months ago by
CandiceChuDVM1.2k
United States/College Station/Texas A&M University
CandiceChuDVM1.2k wrote:

Hi all,

I am writing this tutorial in response to my previous question: NCBI SRA submission: neither sample_name nor biosample_accession are set.

I took me three days to figure our what's going on so I hope my tutorial can save your time and make your life easier:

Tutorial: How to upload your data to the evil Sequence Read Archive (SRA)?

Enjoy.

ADD COMMENTlink modified 10 days ago by Lucila0 • written 4 months ago by CandiceChuDVM1.2k

Thanks for putting this all together.

Right from the start, just getting data in and out of the SRA demonstrates the complete disconnect between the theory and the reality of reproducible research.

ADD REPLYlink written 4 months ago by Istvan Albert ♦♦ 73k

I can't agree more with you.

ADD REPLYlink written 4 months ago by CandiceChuDVM1.2k

Not sure I understand this part:

My files are stored on supercomputer and I am not going to download them to local computer then upload them through FTP.

As you mention elsewhere, it's running linux. In that case, it should have FTP. You can use which ftp to confirm.

ADD REPLYlink written 4 months ago by igor4.4k

Yes. I have tried ftp using the following instruction:

After you login,
1. navigate to your account folder: cd uploads/candicechu@tamu.edu_TsOpWGZR
2. create a subfolder with a meaningful name (required): mkdir new_folder
3. navigate to that folder: cd new_folder
4. deposit your files into that folder: put file_name

However, I found that if I am not going to write a script for the process, it's easy for me to make mistake and get kicked out from the log in status. That's why I choose to use Aspera in which I can only put one line of command to achieve what I want.

ADD REPLYlink modified 4 months ago • written 4 months ago by CandiceChuDVM1.2k

Hi CandiceChuDVM,

thank you so much for this post. It will be very useful.

I would like to ask you one question: Do you know if they have requirements to let you upload you data (in terms of quality and contamination of your samples, for example with adaptors)?

Thank you!

Cheers, Lucila.

ADD REPLYlink written 10 days ago by Lucila0

I don't think they check the contents of your files other than to make sure they are in the proper format.

ADD REPLYlink written 3 days ago by igor4.4k
1
gravatar for igor
4 months ago by
igor4.4k
United States
igor4.4k wrote:

According to NCBI, you should be submitting RNA-seq data to GEO, not SRA:

Functional genomics studies that examine gene expression, regulation or epigenomics (using methods such as RNA-Seq, miRNA-Seq, ChIP-Seq or methyl-Seq) should be submitted to GEO.

Source: https://www.ncbi.nlm.nih.gov/guide/howto/submit-sequence-data/

As an added benefit, it's a much simpler process.

ADD COMMENTlink written 4 months ago by igor4.4k
1

GEO submits raw data to SRA on your behalf automatically (https://www.ncbi.nlm.nih.gov/geo/info/seq.html)

ADD REPLYlink modified 4 months ago • written 4 months ago by genomax31k

Yes, but that part is automated, so you don't have to worry about that as a submitter.

ADD REPLYlink written 4 months ago by igor4.4k

Thanks! I wasn't aware of that. I will contact SRA later to figure out what to do at this point.

ADD REPLYlink written 4 months ago by CandiceChuDVM1.2k
1

If you email GEO, they can link SRA and GEO entries. Or at least they used to.

ADD REPLYlink written 4 months ago by igor4.4k
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