I'm using cutadapt to trim adapter sequences from a small rna-seq dataset. However I'm getting a lot of very small reads after trimming with around 35% being 0 length reads. I'm using the following command:
cutadapt --discard-untrimmed -O 7 --minimum-length=18 --maximum-length=40 -a AGATCGGAAGAGC file.fastq > trimmed_file.fastq
With this settings I'm losing almost half of my data after trimming because they are becoming too short (<18). Am I doing something wrong? It's possible to get sequences reads without inserts (only adapter sequenced)?
Maybe I'm using the wrong sequence adapter, but from what read on foruns the sequence 'AGATCGGAAGAGC' is able to trim all adapters from Illumina sequencing, or am I wrong?
Thanks in advance.
ps: I have tried other overlap settings (3, 5 and 6) and the results are the same.