How to decide which parameter to change for more quality results while trimming with Trimmomatic?

Question

[sam]

How to decide which parameter to change for more quality results while trimming with Trimmomatic? Which parameter is usually most commonly altered?

 PE [-version] [-threads <threads>] [-phred33|-phred64] [-trimlog 
<trimLogFile>] [-quiet] [-validatePairs] [-basein <inputBase> | 
<inputFile1> <inputFile2>] [-baseout <outputBase> | <outputFile1P> 
<outputFile1U> <outputFile2P> <outputFile2U>] <trimmer1>...

[GenoMax]

Partly addressed elsewhere: How do you decide to set the run to SE or PE on trimmomatic?

[Ram]

Stop opening multiple questions addressing the same topic in a short span of time - it is bad etiquette.

[sam]

ok sorry this is my first time using it

[Ram]

Do not delete posts that have received feedback.

Answer 1

[Istvan Albert]

Don't overthink it, I once set my parameters to be

SLIDINGWINDOW:4:30 ILLUMINACLIP:adapter.fa:2:30:5

never needed to change those ... actually, I did change something, I moved to a different tool fastp

• https://github.com/OpenGene/fastp

[sam]

Actually it is a project and we are expected to change parameters:D

[Ram]

Then change them and learn what the project is meant to teach you - what these parameters mean.

[Istvan Albert]

then read the manual and learn what the parameters do