Basic Unix Commands

Why Unix?

Most bioinformatics tools run in a terminal, not a graphical program.
Unix commands let you:

• move around folders

• list and inspect files

• run analysis programs

Navigation (Where am I?)

Before you can analyze data, you must know how to move around the folders (directories).

• pwd (Print Working Directory): Shows your current location.
• ls (List): Shows files in the current folder.
• cd folder/ (Change Directory): Move into a folder.
• cd ..: Move one level up.
• cd ~: Go to your home directory.
• mkdir name (Make Directory): Create a new folder.

Copy and move files

• cp file folder/: Copy file from the first argument (source) to the last (destination).
• mv file folder/: Move file from the first argument (source) to the last (destination).
• rm file: Remove file. Caution: There is no “Trash Can”, Removed files are gone.

Inspecting Files

Never open a ~10GB FASTQ file in a text editor like Word or Notepad. It will crash. Use these instead:

• head -n 20 file.txt: See the first 20 lines.
• tail -n 20 file.txt: See the last 20 lines (useful for checking if a log file finished correctly).

Working with Compressed Data

Bioinformatics data is almost always compressed (.gz) to save space.

• zcat name.fastq.gz | head: View the top of a compressed fastq file.
• gzip file: Compresses a file and adds a .gz extension.
• gunzip file.gz: Decompresses the file.

Counting and Searching

• wc -l file.txt: count lines.
• grep "searchterm" file.txt: find lines containing a word.
• grep -c "^@" file.fastq: Count how many sequence headers (starting with @) are in a file.