Hi,

I am using Trim Galore! to trim my small RNA fastq files. with the code below. However, the output in multiqc shows that I remove the small_rna adapters BUT retain universal Illumina adapters. When I do not use the option --small_rna it removes the universal Illumina adapters but keeps the small_rna adapters. Any idea how I can make Trim Galore! trim both adapters?

#!/bin/bash


    for i in $(ls *R1* | sed s/_R1.fastq.gz// | sort -u); 

    do

    trim_galore --paired ${i}_R1.fastq.gz ${i}_R2.fastq.gz -q 20 -o ./galore-trimmed_small_rna --fastqc --cores 6 --stringency 3 --small_rna

    done