Do you want to:
chmod -R 0644 application system index.php
Assuming that CI is installed in the root directory of the website, with the application/ and system/ directories located there, which is the default setting.
What I usually do is put the application/ and system/ directories outside the root of the website when I use Codeigniter, after which you need to edit the index.php file to reflect this:
$system_path = '../system'; $application_folder = '../application';
Note that you add ../ (and should also move these directories one level down), but I'm distracted. Permissions for each directory should be 0755 and for each .php file 0644, wherever you put them. This includes any supplier, third party, sparks, etc. And any custom asset layouts.
If you use some kind of template engine, good settings will work with permission resolutions 0755 in the place where the engine writes its output and intermediate output, if applicable. If you find this violation, find a host that supports suexec, so you do not need to make these places 777 (or write to the world).
This is easiest done with a terminal (SSH), but can also be easily done with any file manager that your host can support.