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Options panel
The Stats tab displays information output by either MELT or TIPseqHunter regarding the currently selected insertion.
Sets whether the main visualization is showing histograms or individual reads.
Currently, individual reads can only be viewed for the junction regions between the mobile element and the reference genome.
- black characters indicate that the bases match the reference sequence
- Red text shows soft clipped bases
- Orange characters indicate substitutions
- Brown 'X' characters indicate deletions
- Underlined characters indicate that an insertion is present to the right of the character
- Hovering the mouse over the underlined character will display a popup showing the inserted sequence
This panel controls which histograms are displayed in the visualization.
Genome reads are reads that do not have any overlap with the mobile element Mobile reads are reads that overlap entirely with the mobile element Junction reads are reads that overlap the junction regions between the mobile element and the reference genome
Bridging indicates that in a read pair one read aligns to the reference genome on the five prime end of the mobile element and the other aligns to the three prime end of the insertion
Toggling the checkboxes will either display or hide the relevant histograms.
The style tab controls the type of plot being shown by the histograms
Stacked histograms have the base set to zero. Stacked histograms can result in neighboring histograms of the same type not aligning correctly, especially around the junction regions.
The stream plot attempts to keep each class of histogram being displayed aligned and as continuous as possible. The stacked plot is zero centered.