Downloading SRA data

Question

[angus.j.g.campbell]

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?

[Michael]

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.

[angus.j.g.campbell]

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

[angus.j.g.campbell]

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

[GenoMax]

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

Answer 1

[Istvan Albert]

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

[angus.j.g.campbell]

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

[Istvan Albert]

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