Functions
Main Functions
Searching and Moving Menu-1(in right Fig.)
Search the position by physical position, annotation ID or free words.
Zoom In and Out Menu-7
TASUKE shows Variant and Depth information with various scales, 1bp to 100kb per block. This level can be changed in Block size menu or simply double click on the position to be zoomed in the main field. Short cut keys ‘+’ and ‘↑’ for zoom in, and ‘‐‘ and ‘↓’ for zoom out are available.
View Mode Menu-2
View mode can be selected from "Frequency" or "Absolute position". Combinations of Depth, SNP and INDEL can be selected to show. Switching depth track to general purpose(Custom) track.
Showing Variant Effect Menu-4
Variant Effect information added by snpEff can be shown by clicking the "Tools"-"snpEff" menu. “About” menu under “snpEff” menu refers the correspondence of colors and levels of effects.The indicator in the main field also shows the relations.
Analysis Menu-4
Several genomic analysis can be run from “Analysis” menu. Primer pairs can be design by using Primer3. And phylogenetic tree can be get by using PHYLIP.
Export Menu-4
An image of currently shown region can be exported as <.png> file from “Export” menu. And FASTA and a variant list of selected region can be downloaded.
Short cut keys Menu-6
Basic actions and short cut keys are shown in ”Manual” window of “Help” menu.
Other options
View options Menu-3
| Block options | Number of blocks, its height and width can be adjusted. |
|---|---|
| Accession manager | Accessions and optional information such as origin and varietal name can be changed. |
| Track manager | Tracks to be shown, their order, color of the structure and number of rows can be changed. |
| Color manager | Block color definition and color gradient can be changed. |
| Theme | Color pattern can be selected from ‘DARK’, ‘SLATE’ and ‘LIGHT’. |
| Indicator ON/OFF | Show and hide the indicator of depth and variant frequencies. |
| Amino acids ON/OFF | Show and hide the amino acid sequences in 1bp scale resolutions. |
| Feature IDs ON/OFF | Show and hide the feature ID on GFF track. |
Tools options Menu-4
| Variant Filter | Filter variants by depth of all reads, alternative (non-reference type) allele reads and genotyping quality. |
|---|---|
| Highlight DEPTH=NULL ON/OFF | Highlight the depth = null (unmapped) site. |
Reset Menu-5
Reset all the setting to default values.