How to decide which parameter to change for more quality results while trimming with Trimmomatic?
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>...
1 answer
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
• 0 views
•
link
written
by
Istvan Albert
then read the manual and learn what the parameters do
• 0 views
•
link
written
by
Istvan Albert
Log in to answer this question.
More posts like this
-
Error: Trimmomatic Command not found
written by Tundup •
-
MultiQC doesn't produce data for all samples, why? (trimmomatic)
written by john •
-
single end Trimmomatic
written by gina02 •
-
Trimmomatic errors
written by marion.ryan •
-
Trimmomatic 0.39 Permission denied accessing fastq.gz
written by e.wing •
-
Trimmomatic couldn't generate output file
written by leukippus0116 •
-
Trimmomatic paired-end mode question
written by slin023 •
-
What is Trimmomatic -validatePairs, and how to use it?
written by jon.brate
-
Trimmomatic 0.36 not acknowledging commands in MacOS terminal in SE mode
written by msimmer92
-
k-mer overrepresentation of WGS Illumina reads
written by Anand Rao
Partly addressed elsewhere: How do you decide to set the run to SE or PE on trimmomatic?
Stop opening multiple questions addressing the same topic in a short span of time - it is bad etiquette.
ok sorry this is my first time using it
Do not delete posts that have received feedback.