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 (Image utilities_closed_16_n_p) | Tracks (Image track_tools) | Track Conversion (Image track_conversion_folder_closed_16_h_p) | Convert from Tracks (Image convert_from_tracks_16_n_p)

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).

Image convert_from_tracks_step2
Figure 27.20: A reads track and two annotation tracks are converted from track format to stand-alone format.

Image convert_from_tracks_output
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.

Image convert_from_tracks_ref_step2
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".

Image convert_from_tracks_ref_output
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 (Image sequence_dna)
Will be created when a sequence track (Image sequence_track_16_n_p) with a genome with only one sequence (one chromosome) is provided as input
Sequence list (Image dnalist_16_h_p)
Will be created when a sequence track (Image sequence_track_16_n_p) with a genome with several sequences (several chromosomes) is provided as input
Mapping (Image contig)
Will be created when a reads track (Image read_track_16_n_p) with a genome with only one sequence (one chromosome) is provided as input.
Mapping table (Image multicontig)
Will be created when a reads track (Image read_track_16_n_p) with a genome with several sequences (several chromosomes) is provided as input.
In all cases, any number of annotation tracks (Image annotation_track_16_n_p)/ (Image variant_track_16_n_p) can be provided, and the annotations will be added to the sequences (reference sequence for mappings) as shown in figure 27.21.