Convert from Tracks
Tracks are useful for comparative analysis and visualization, but sometimes it is necessary to convert a track to a normal sequence or mapping. This can be done with the Convert from Tracks tool that can be found here:
Toolbox | Utility Tools (
) | Tracks (
) | Track Conversion (
) | Convert from Tracks (
)
One or more tracks can be used as input. In the example given in figure 27.20 a reads track and two annotation tracks are converted simultaneously to an annotated read mapping (figure 27.21).
Figure 27.20: A reads track and two annotation tracks are converted from track format to stand-alone format.
Figure 27.21: The upper part of the figure shows the three individual input tracks, arranged for simplicity in a track list. The lower part of the figure shows the resulting stand-alone annotated read mapping.
Likewise it is possible to create an annotated, stand-alone reference from a reference track and the desired number of annotation tracks. This is shown in figure 27.22 where one reference and two annotation tracks are used as input.
Figure 27.22: A reference track and two annotation tracks are converted from track format to stand-alone format.
The output is shown in figure 27.23. The reference sequence has been transformed to stand-alone format with the two annotations "CDS" and "Gene".
Figure 27.23: The upper part of the figure shows the three input tracks, shown for simplicity in a track list. The lower part of the figure shows the resulting stand-alone annotated reference sequence.
Depending on the input provided, the tool will create one of the following types of output:
- Sequence (
) - Will be created when a sequence track (
) with a genome with only one sequence (one chromosome) is provided as input
- Sequence list (
) - Will be created when a sequence track () with a genome with several sequences (several chromosomes) is provided as input
- Mapping (
) - Will be created when a reads track (
) with a genome with only one sequence (one chromosome) is provided as input.
- Mapping table (
) - Will be created when a reads track () with a genome with several sequences (several chromosomes) is provided as input.
)/ (
) can be provided, and the annotations will be added to the sequences (reference sequence for mappings) as shown in figure 27.21.