Trimmomatic 0.39 fails for adapters
I'm trying to trim my RNA-Seq FASTQ files, but it's not working..
The parameters I'm using are:
java -jar ~/Applications/Trimmomatic-0.39/trimmomatic-0.39.jar SE -phred33 shock02_RNASeq.fastq.gz trimmed_shock02.fastq.gz LEADING:3 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36 ILLUMINACLIP:TruSeq3-SE.fa:2:30:25
Here you are the results, can you help me out? Which parameters should I try to change to trim the adapters?
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Istvan Albert
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pinheirofabiano •
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pinheirofabiano •
1 answer
You are trimming with Illumina adapters rather than polyG,
add the polyG sequence into the adapter fasta file (basically just a bunch of Gs), and cut it with say at least 8 Gs
As GenoMax also stated, you should use fastp instead it is a much better adapter cutting tool.
It has many options to cut polyG and set the minimum length for cutting and so on.
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It is difficult to see if the plot shows presence of
poly-GorIllumina universal adapter. You may want to trybbduk.sh(guide; https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ ) orfastpas alternatives.