Question: Downloading SRA data
0
gravatar for angus.j.g.campbell
2 days ago by
angus.j.g.campbell0 wrote:

I am a new graduate student jsut beinging in a bioinformatics program so computational work is new to me. I have downloaded the SRA toolkit from the link here: https://www.ncbi.nlm.nih.gov/sra/docs/sradownload/

I am usign the windows command prompt and it is not recognizing the package. Do I need to download a bash shell for windows? I made sure it was in the proper directory when I extracted it in the c:\Users\user. Do I need to be located in the bin directory?

rna-seq sra • 74 views
ADD COMMENTlink written 2 days ago by angus.j.g.campbell0
1

Did you follow the instructions here? https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-Toolkit

There is a quick test of fastq-dump.

ADD REPLYlink written 2 days ago by Michael Dondrup48k

Thank you for directing me to this resource. I will try this and see what mistakes I made.

ADD REPLYlink written 2 days ago by angus.j.g.campbell0

the configuration gui for SRA toolkit, local directory

I have gotten to this point where I want to set the directory to put the data I download but it is not clear how to get the configuration to accept. Pressing enter takes me out of the GUI for setting the path and does not save my choice. It says OK but pressing o or k does not do anything. Its not really clear how to actually make the selection I want.

Screen shot is here, my image does not appear to be loading correctly. https://ibb.co/Z2L0H8Z

ADD REPLYlink modified 2 days ago • written 2 days ago by angus.j.g.campbell0
1

You can press tab to move around the various options (until you get to the OK).

ADD REPLYlink written 2 days ago by genomax92k
0
gravatar for Istvan Albert
2 days ago by
Istvan Albert ♦♦ 85k
University Park, USA
Istvan Albert ♦♦ 85k wrote:

If you intend to work in bioinformatics install the Linux Subsystem and work from there. There is no point in puttering around in windows prompt, sooner rather than later you'll have to use Unix anyway

ADD COMMENTlink written 2 days ago by Istvan Albert ♦♦ 85k

Thanks I've installed the ubuntu bash terminal for windows. Is that the best option in your opinion?

ADD REPLYlink modified 2 days ago • written 2 days ago by angus.j.g.campbell0
1

The Linux Subsystem for windows allows deploying various Linux distributions. Ubuntu is a good choice.

ADD REPLYlink written 2 days ago by Istvan Albert ♦♦ 85k
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