Use of Tablet

Previously, I used jbrowse to find that some information is not displayed accurately, such as browsing a BAM file. At a certain point, the depth is 1000, but the browser displays less than 1000, and the read is often missing. Therefore, give up jbrowse and use tablet. After comparison, it is found that the tablet display is correct where the jbrowse display is incorrect.

In addition, tablet can be used in windows. It is easier to install without any configuration files. The following describes how to use tablet.

First, import your reference sequence. CTRL + O

Then drag your Bam file to the software. Note that the BAM file also requires the index file.

Tablet is the same as jbrowse. Only one sequence can be viewed at a time. In the leftmost contigs browser panel, select the sequence you want to view.

In addition to the contig name, there are also reads numbers and contig lengths. The filter option is shown below to show only the contig you want to view.

The rightmost side of the Panel is the search, that is, you can search for reads or subsequence. Under the combo box, you can choose whether to search for the current contig.

If you select ignore pads when seaarching.

The search term acgt will match the following sequences:

A	C	G	T
A	C	*	G	T
A	C	*	*	*	*	G	T
A	C	N	G	T

 

Overview panel displays coverage and other information. Enable and disable the Panel in advanced:

You can also adjust whether to display coordinates and the display mode of coverage. Coverage can be displayed in two ways: scaled Data Overview (not precise) and coverage Overview (more precise display ). Right-click to select the coverage mode, or click scaled and coverage in advanced.

In the overview panel, click the left mouse button to quickly get to the desired place. You can see the location of the red box. You can also drag the red box to move it.

 

You can directly view the comparison information under the overview panel. You can select a mode in color schemes, such as the nucleotide mode, read type mode, and direction mode. The help information is displayed when you move the cursor over each mode.

The bar above the coverage is Bam bar, the white bar represents the current position, and the gray bar represents the previous position.

Right-click a base, and you can select outline: With read (enclose the base's read), row (enclose the whole row of the base ), column (enclose the entire column of the base ). Cancel all tags select clear all.

Click and hold the left button to drag the mouse. You can press Ctrl to scroll the scroll wheel.

 

If you hover the mouse over a read, The read information is displayed. The precursor is read info open:

The floating information contains the read name, starting from, whether the read is forward (green) or reverse (blue ). If the data is written red-end, 1/2 indicates the first read, and 2/2 indicates the second read.

 

Unfortunately, it cannot be located. For example, if I want to see the situation at the 1234435 coordinate, I must manually move it to find the location, rather than directly entering it like jbroswse...

For more detailed instructions, please refer to the official website: http://bioinf.hutton.ac.uk/tablet

 

By freemao

Fafu

[Email protected]