Page Comparison

Background and external resources

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You can also use SRA Explorer to view all files in a project and download all or some of them: https://www.biostars.org/p/385930/

Goal

Download public data deposited in NCBI’s Short Read Archive (SRA) database.

Pre-requisites (if not available)

• Installed conda3 or miniconda3 ( https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html )

• Basic unix command line knowledge (example: https://researchcomputing.princeton.edu/education/external-online-resources/linux ; https://swcarpentry.github.io/shell-novice/ )

• Familiarity with one unix text editors (example Vi/Vim or Nano):

  • VIM ( https://bioinformatics.uconn.edu/vim-guide/ ; https://missing.csail.mit.edu/2020/editors/)

  • Nano (https://engineering.purdue.edu/ECN/Support/KB/Docs/BasictutorialforNanou ; https://www.howtogeek.com/howto/42980/the-beginners-guide-to-nano-the-linux-command-line-text-editor/ )

Installing miniconda

https://docs.conda.io/en/latest/miniconda.html#linux-installers

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Download SRA files

Example: PBS script (launch_fetch_SRAfiles.pbs) to fetch multiple files from SRA database

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