miRNA analysis is new for me. I'm working on reads from a 55 cycle single-read sequencing run and I think I have a problem.. After pre processing steps (removing low quality reads, removing 5' and 3' adapters), 50% of the reads are 55 nucleotides long (that's mean around 1000000 on a total of 2000000).
I understand that these reads should be removed, as they can't be miRNA, but is it normal that length filtering implies removing such a number of reads? and to what could these reads correspond?
Thanks in advance for your help!