ReadXplorer main window with one opened reference and three (two of them are visible) opened track data sets. The mapped reads are classified into three different mapping classes (green - perfect match, yellow - best match, red - common match).
The Alignment Viewer shows all read alignments including mismatches and gaps. The tooltip shows details for the hovered read alignment.
The Histogram Viewer supplies intuitive exploration of position specific coverage information as histogram. The match coverage is shown in green and all mismatches and gaps are displayed in a base specific color.
The Read Pair Viewer displays the pair configuration of all aligned reads. Perfect Pairs are displayed in green, while Distorted Pairs are yellow and Single Mappings are red. The pair configurations are computed by a well-defined algorithm in ReadXplorer.
The Thumbnail Viewer allows inspecting the coverage of selected features (e.g. genes) among selected tracks. It enables an easy comparison of different experiments (different tracks).
The Double Track Viewer visualizes the coverage differences between exactly two tracks.
The Multiple Track Viewer combines the coverage of an arbitrary number of selected tracks in one data set. Combinations of tracks can also be used for any of ReadXplorer's automatic analysis functions.
All relevant SNP information is shown in the table. For detailed visual inspection, the selected SNP position is automatically centered in the data viewers (here: Histogram Viewer).
A differential gene expression result using DESeq within ReadXplorer with a result table and an interactive M/A plot. The selected gene is automatically centered in the synchronized viewers (here: Reference and Track Viewers).
Result of a Transcription Start Site (TSS) detection. This analysis includes novel transcript detection capabilities. In this example, the start of the gene is annotated correctly.
Result of an RPKM and read count analysis. The histogram shows the distribution of RPKM values on the number of genes (log scale). The tooltip displays the actual count of features, which belong to a histogram bar.
An operon detection result based on the number of spanning reads of two neighboring genes. The table lists each neigboring pair of genomic features in one row as "Feature 1" and "Feature 2".
The Feature Coverage Analysis enables detection of all reference features that show predefined characteristics in terms of their coverage. E.g. the shown feature is covered to 15% with more than 4 reads at each position.
The Coverage Analysis enables detection of all reference intervals that show predefined characteristics in terms of their coverage. In this example all reference intervals without any mapped reads are listed.
The RNA secondary structure prediction can be used either to calculate the most probable secondary structure of a selected sequence from the reference or from a selected alignment in the Alignment Viewer.