Reviewing Sequencing Information
Users can use the file review plot nodes to visually inspect and analyse the results of their sequencing experiment. There are currently six plot types in total available.
The side menu is used to select all the different options that can be displayed. Users must first select the plot they are interested in. Then if normalisation has been performed, they can also select each normalisation they are interested in to view its resulting effect on the plot.
In plots that show individual file information the sample name with an underscore and a number is used to denote the sample and its corresponding replicate number (i.e Sample1_1 would be the first replicate for sample 1).
In addition, several of the plots have extra options available to them. Those are detailed below.
Box plots show the interquartile ranges of a set of small RNAs from each replicate file. The window slider allows the upper and lower abundance values to be changed on the fly by the user. The plot options menu will allow users to select desired annotations on the fly.
Size Class Distribution
The size class distributions for each replicate file. The user can choose to show redundant (all data) non-redundant (individual sequence counts) and the complexity (redundant/non-redundant counts).The plot options menu will allow users to select desired annotations on the fly.
M Versus A Plots
These diagrams plot fold change values per small RNA sequence versus average abundance for that sequence. Users can choose between the MA values or the correlation plot. The plot options menu will allow users to select desired annotations on the fly.
Fold Change Box Plots
These present the interquartile ranges of fold changes over all sample combinations. Additional plots showing the effect any performed normalisations on those ranges has. The plot options menu will allow users to select desired annotations on the fly.
Mapping Quality plots are given to show the non redundant and redundant counts or complexity values for sequences that match the genome. Users can use the plot options to switch to a percentage view.
The table of values calculated using the Jaccard similarity index. Users can compare normalised versions of each table using the side menu.
The composition of nucleotide characters for all sequences at each position separated by size class. Orange bands track the nucleotide T across the sequence range, Red bands track the nucleotide G, Blue bands track A and Greentracks C.
Users can use the plot options on the side menu to change the current file being viewed. Actual file names are given in this menu.