Hello Kian!

Questions similar to yours can already be found at:

• Fastq Quality Control Shootout
• Manipulate Sequences In Fastq Files
• Brief Reminder On How To Ask A Good Question
• trimming fastq files with Trimmomatic

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

P.S.: Reading the manual (and google) also helps.

What was unclear after reading the manual?

If you want to do this because of the positional bias that you are seeing then don't worry. There is no need to remove those bases.