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?
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
Thanks I've installed the ubuntu bash terminal for windows. Is that the best option in your opinion?
The Linux Subsystem for windows allows deploying various Linux distributions. Ubuntu is a good choice.
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Hello, welcome at Biostars. That is a bit of an unspecific question. Please read the manual first, follow all instructions, and if something is then still unclear please use
editand add details to your post.Also check Fast download of FASTQ files from the European Nucleotide Archive (ENA)
Hi there I am sorry to have such an unspecific question but the directions are not clear and I am getting stuck.
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.
Thank you for directing me to this resource. I will try this and see what mistakes I made.
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
You can press
tabto move around the various options (until you get to the OK).