# What are the right parameters to trim a small RNA transcriptome with trimmomatic?

I'm having some problems with finding the right parameters to trim my small RNA Illumina reads (51 nt long) with Trimmomatic.

Before trimming, one of the samples (21M reads) looks like this:

So for my understanding, it's quite good and the last two issues can be easily solved with adapter trimming.

I then tried to trim it with the command

java -jar /opt/Trimmomatic-0.38/trimmomatic-0.38.jar SE -threads 24 -phred33 FemaleMito3.fastq FemaleMito3_trimmed.fastq ILLUMINACLIP:adapters.ultimate.fa:2:30:10 AVGQUAL:25 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:18


but I got the following result:

So now I have a problem with the sequence quality per tile (why?), an overall drop of the quality at the end of the reads and a warning with the sequence length distribution.

Then I tried trimming just the adapters with this command:

java -jar /opt/Trimmomatic-0.38/trimmomatic-0.38.jar SE -threads 24 -phred33 FemaleMito1.fastq FemaleMito1_noadapters.fastq ILLUMINACLIP:adapters.ultimate.fa:2:30:10 AVGQUAL:25


but again I get some new issues:

Again the per tile sequence quality issue, and now a warning about the GC content.

I didn't find anywhere some precise instruction on how to trim a small RNA library with Trimmomatic. How should I properly trim my small RNA library with Trimmomatic?

• Jul 16, 2019 at 13:30