All information in tracks is tied to genomic positions. Thus, all tracks being used for a particular analysis or in a track list must be based on the same coordinate system. That coordinate-system is provided by a reference genome. Tracks based on the same coordinate system, that is, the same reference genome, can be analyzed and viewed together in a meaningful way.

This means that it is vital that files containing genome coordinates, such as BED files, be imported against a reference track with the same coordinate system.

This FAQ addresses how to check if tracks are compatible and how to obtain compatible tracks if they are not.

Check compatibility of existing tracks by making a track list

If you can make a track list with a set of tracks, then those tracks are compatible, and could be used together in an analysis. To do this, go to: 

File | New | Track List

and select the tracks of interest.

If a track is incompatible with others selected, you will see a message in the wizard saying "Select tracks from same genome".

 

What to do if a track is incompatible with other tracks of interest

For standard reference data, such as hg38 annotations, we suggest one of these routes:

• Use the CLC Genomics Workbench Reference Data Manager, and download the reference data of interest. This may be either individual elements from the relevant reference data set, or a full reference data set. Within a set, all the tracks are compatible.

OR

• Import the data as a track , using the desired reference genome, already imported, as the reference track during import. 

 

For custom data, for example target regions of interest:

• Import the data as a track, specifying the relevant reference genome track during import, and
• After import, check that the target regions are located where you expect by making a track list containing the newly imported track and other relevant tracks.

For example, for a target region track imported from a BED file, include it in a track list with mRNA or CDS annotation tracks. Check the target regions are placed where you expected, particularly near the end of the chromosomes, as any coordinate mismatches will be most obvious there.