From the adaptor-trimmed single-end microRNA-Seq datasets, I observe that there are three peaks in terms of the read length.
1) peak 1 at 11bp;
2) peak 2 at 22bp;
3) peak 3 at 43bp.
The 22bp peak should indicate the enrichment of microRNA species.
But how about 11bp peak and 43bp peak? Is it normal to have three peaks for microRNA sequencing? Where do the peak1 and peak3 come from?
Is it important to select the read length, for example, only choose read length of 18bp-26bp for the downstream analysis such as quantification and differential expression analysis? If so, which tool can be used to select the read length?
If read length selection is done, it appears only a small proportion of the total reads from the experiment are from microRNA species. Is this generally accepted? What percentage would make sense?