I have single ended 75 bp miRNA reads (Quiagene miRNA kit) reads with UMI.
The fastqc report shows high peak at the 83-84 bp and illumina universal adaptor.
After removing the 5-3' adaptor ((5’-3’) AACTGTAGGCACCATCAAT) and also reads lower than 17bp with cutadapt, The sequence distribution peak is on 22-23.
I know that miRNA should be around 18-22 and UMI length 12. Doesn't it mean that I should see a peak around 30-34?
The code that I used was:
cutadapt -a AACTGTAGGCACCATCAAT --minimum-length 17 -o tri.fastq sample.fastq