Decompressing the file
Does your file have .gz on the end of its filename? And how big is it? You can ls -lh to find out:
ls -lh ./
You'll see something like:
-rw-r--r-- 1 user group 57M 11 Oct 14:09 gencode.v41.annotation.gff3.gz
This file is 57 megabytes big and ends with .gz. (If you're doesn't have .gz on the end and looks bigger -
don't worry. It's likely your operating system has decompressed it for you.)
If you have that .gz ending the file has been compressed with gzip. We could work directly with it, but to
make life simple let's decompress it now:
gunzip gencode.v41.annotation.gff3.gz
Note
If you're bored typing the filename - just type the first few letter and press tab to auto-complete it.
Use ls -lh to see how big it is now. You should see that it's lost the .gz ending and now is about 1.4
gigabytes (i.e. bytes) big. So gzip compressed it by about 24 times!
Aside on using the compressed file
As it happens, much of this tutorial could be carried out directly using the gzipped version of the
file as well. Instead of using cat, less, and grep in the next few pages, for example, we
could use zcat (or gunzip -c), zless, and zgrep. For other commands like awk we would
need to build pipelines that decompress the file first. This all works fine and helps save disk
space.
But for the purposes of this tutorial we'll work with the decompressed file for simplicity.