Course Details

  • Date: September 27th, 2018 - September 27th, 2018
  • Time: 10:00 am - 4:00 pm
  • Location: NIH Bldg 10, FAES Room 4 (B1C205)
  • Presenter(s): Amy Stonelake (BTEP), Peter FitzGerald (GAU)
  • Course Number: 1003

Sept. 27, 2018: BTEP: Practical Bioinformatics Skills at the Command Line

Please bring your own laptop to the class or indicate in the comments if you need to borrow one of our loaner laptops.

Confused about the command line? Working with data on your laptop that needs to be on the NIH Biowulf cluster for further analysis? Want to transform your BCL files into FASTQ, or turn your BLAST results into an Excel Spreadsheet? Help is available.

1. This will be a hands-on workshop with step-by-step instructions provided.
2. Learn basic unix commands for creating files, moving around the directory tree, running programs on the NIH Biowulf cluster.
3. Use tools like Globus Connect, scp (WinSCP) to move files from your laptop to Biowulf and back.
4. Understand more about various file formats, how they are related, and learn how to transform from one file type to another.
5. Read from and write to files on Biowulf.
6. Compare the web version and command-line versions of NCBI BLAST tools.

Course Material 1:  Handout-for-Practical-Bioinformatics-Skills.docx

Course Material 2: PDF icon fwunixref.pdf

Course Material 3: PDF icon sequencers.zip

Course Material 4:  Practical-Bioinformatics-Skills.pptx