Windows / Linux characters

I am running programs on a Windows/Linux hybrid network and have come across some newline issues. What is the best way to read a file and make sure that it conforms to the native characters? That is, how should I convert a Windows file to Linux format on Linux and vice versa?
Thank you

1) Always explicitly specify the character encoding used when writing text - I use utf-8. Don't rely on the default.
2) Always explicitly specify the EOL - I use "\n" which works with just about anything on both Linux and Windows except for Notepad.

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