I have UMI extracted miRNA reads which I want to analyse using mirDeep2 for known and novel miRNA discovery. But when I give these as input, mapper.pl collapses reads drastically and brings down 7 million reads to 1200 reads with count tag on each read.
1) Is there a way to retain UMI information on the Fastq header so as to do deduplication later post alignment by mirdeep2?
2) Has anyone successfully analyzed UMI tagged miRNA data using mirDeep2?
Thank you, Pratibha.