You might use a wrong adapter sequence for 3' adapter trimming. The library could be Illumina TruSeq RNAseq, or others.
The most direct way is to check the library preparation protocol or ask the one who did the experiment.
If not, you can guess the adapter anyway.
Have a look at the Summary in the
cutadapt log. What are the number
Reads with adapters: ... (xx.x%)? (varies depend on your insert size and library quality. it could be 75%, 99% for my data).
Prepare a subsample for testing
# 10k reads
$ head -n 40000 raw.fq > demo.fq
First, you can test the following 2 adapters, using
# TruSeq small RNA library
$ cutadapt -a TGGAATTCTCGGGTG -m 18 -o demo-cut1.fq demo.fq > cut1.log
# TruSeq RNAseq library
$ cutadapt -a AGATCGGAAGAGCAC -m 18 -o demo-cut2.fq demo.fq > cut2.log
Any way, you can guess the adapter using
$ fastp -i demo.fq -o trimmed.fq
Detecting adapter sequence for read1...
>Illumina TruSeq Adapter Read 1