Trimmomatic 0.39 fails for adapters

Question

[pinheirofabiano]

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?

[GenoMax]

It is difficult to see if the plot shows presence of poly-G or Illumina universal adapter. You may want to try bbduk.sh (guide; https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ ) or fastp as alternatives.

Answer 1

[Istvan Albert]

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.