Deleting loaded data can be done in multiple ways. The main command verb is delete. It is used with different objects depending on what you are going to delete. The most typical commands are delete mapset and delete tracktreenode.

Note that if you plan to hide a map set from the view, you don't need to delete it, but make it "inactive". Use the command edit mapset and set its IsActive flag to false.

Deleting a map set with all its maps and tracks is done by running the command

delete mapset <mapset> [-t]

Every command 'delete' will list the counts for the objects to be deleted and will ask for a confirmation before actually deleting the data:

PS> delete mapset "Glycine (genus)/Glycine max/Wm82.a4.v1"
Deleting map set /Glycine (genus)/Glycine max/Wm82.a4.v1 (Id:34)...
This operation will affect:
  - 1 mapset (/Glycine (genus)/Glycine max/Wm82.a4.v1)
  - 282 maps
  - 0 map qualifiers
  - 20 chromosomes
  - 282 sequences
  - 1,290,280 annotations
  - 0 alignments
  - 0 mappings
  - 0 VCF data blocks
  - 0 studies
  - 0 qtls
  - 0 ribbons
  - 2 map set qualifiers
  - 0 quantitative tracks
  - 360,762 orthologs

Do you want to delete the mapset? (Y/N)

The map set can be defined by MapSetId (use the command list mapset to find the ID) or by its path in the map set tree (see the example above).

One word about deleting loaded tracks. A track is a collection of mapped features (genes, markers, etc.) on a single map. The tracks can be grouped under parent nodes, and such a hierarchy is common for all maps of the map set. The nesting structure can be shown by the command list tracktree. Accordingly, to delete all tracks with the same name on all maps of the map set, or a track node, use the command 

delete tracktreenode <mapset>

Here is an example where the list of avaiable track nodes is presented in response to the delete command. You will need to select the track name by typing its [node number].

PS> delete tracktreenode 2
TrackTree for MapSet 'Os GJ-temp: IRGSP-1.0 (Nipponbare)':

[0] RNA-seq (Group, Order: 0)
    [1] RNA-seq leaf (Track, Order: 7, Type: Quantitative)
    [2] RNA-seq panicle (Track, Order: 8, Type: Quantitative)
    [3] RNA-seq root (Track, Order: 9, Type: Quantitative)
    [4] RNA-seq mature_leaf_SRR10751914 (Track, Order: 10, Type: Quantitative)
    [5] RNA-seq mature_leaf_SRR10751915 (Track, Order: 11, Type: Quantitative)
    [6] RNA-seq panicle_SRR10751910 (Track, Order: 12, Type: Quantitative)
    [7] RNA-seq panicle_SRR10751911 (Track, Order: 13, Type: Quantitative)
    [8] RNA-seq root_SRR10751912 (Track, Order: 14, Type: Quantitative)
    [9] RNA-seq root_SRR10751913 (Track, Order: 15, Type: Quantitative)
    [10] RNA-seq young_leaf_SRR10751908 (Track, Order: 16, Type: Quantitative)
    [11] RNA-seq young_leaf_SRR10751909 (Track, Order: 17, Type: Quantitative)
[12] MSU gene models (Track, Order: 0, Type: Annotation)
[13] Inversions (Track, Order: 0, Type: Synteny)
[14] Transposable Elements (Track, Order: 0, Type: DenseMarker)
[15] Gnomon gene models (Track, Order: 1, Type: Annotation)
[16] HDRA_3k_validated (Track, Order: 2, Type: GenericBp)
[17] FGENESH gene models (Track, Order: 3, Type: Annotation)
[18] Predicted TSS (Track, Order: 5, Type: GenericBp)
[19] Tags (Track, Order: 6, Type: GenericBp)
[20] Gramene Gene models (Track, Order: 18, Type: Annotation)
[21] genes from CSHL (Track, Order: 20, Type: Annotation)

Enter [NodeNumber] to delete:

Removing other object types, such as variants, synteny, orthologs, etc., can be done by other delete commands described on a separate page.