I'm doing a microRNA-seq analysis. After trimming and checking the results in FastQC the sequence length distribution panel shows two peaks at 24 nt and 36 nt. Here is my trimming command:
cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -e 0.1 -O 5 -o H28_trim_test3.fastq H28.fastq
after aligment with mirdeep2 (with the help of the mapper.pl + quantifier.pl modules) I've got 0.62/0.38 mapped/unmapped ratio.
I'm just wondering if this aligment ratio is acceptable for mammalian microRNAs or should I improve the mapped ratio? Also if I can abolish somehow the 36 nt peak will that improve the mapping ratio? I think yes, but I can't figure out the way yet.