Trimmomatic - default settings?

[Zapages]

Hi all,

I was wondering if someone could kindly share some of their traditional or "default" settings should a person use for Trimmomatic, which have worked for their Trimmomatictasks. I am going to try to use it for the first time and I was wondering what setting I should use.

1) seed mismatches
2) palindrome clip threshold
3) simple clip threshold

4) Sliding window.

Thank you,

Zapages

[mastal]

The trimmomatic web page gives examples for use with SE or PE reads which should answer your questions.

http://www.usadellab.org/cms/?page=trimmomatic