Basic Statistics: Overview
Basic Statistics: Main plots
This plot shows the initial number of reads that remain after the main processing steps of the analysis workflow. The first bar 'Initial number of reads' shows the total amount of reads produced by the sequencer for this sample (100%). The second bar 'Length filtering' depicts the number of reads left after filtering for reads that are too short or too long (default thresholds for removal are <32 nt and >15 nt). The third bar 'Unique mapping' shows the number of reads that are uniquely mapped to one of the five small RNA databases or the respective genome (reads shorter than 20 nt with 0 mismatches, longer than 20 nt with 1 mismatch).
This plot shows the percentage of uniquely aligned reads per small RNA species. RNA species considered are miRNAs, piRNAs, snoRNAs, snRNAs, and rRNAs. Additionally, RNAs that could not be aligned to known small RNA species but that map uniquely to the genome are shown in the 'miscRNA' bar. These RNAs are either fragmented long or short RNA species, editing variants of small RNAs (isoMIRs), or might represent as yet unknown small RNA species. An analysis routine for the classification of 'miscRNAs' will be included in the second version of the software.
This plot shows the distribution of sequence length after adapter removal (trimming) and before length filtering. This plot allows you to draw general conclusions about the success of your sequencing experiment. Peaks that you should be seeing, depending on the sample source, might be a prominent peak around 20-23 bases, which is the general size distribution of miRNAs. Other small RNA species show peaks around 31-32 bases for snoRNAs and piRNA. A prominent peak at 0-1 bases would indicate adapter ligations without insert, this would mean that your DNA input into the ligation reaction was too low or the amount of adapters was too high, parameters that should be adjusted in the next library preparation. A prominent peak around 14-15 bases might indicate degradation products, either real degradation products in the cell or fragments of RNA due to the sample preparation. Peaks that appear around 50 bases indicate that the size selection reaction was bad or did not take place and in general represent regular, larger RNA species.
