Besides the description of tracks that can contain verbose information, the system allows assigning short track qualifiers. These key-value pairs can help categorizing the tracks and facilitate the search in a large list of tracks. The specialized interface in webPersephone allows filtering the tracks based on different criteria, which is important as a map set potentially can have thousands of tracks. For example, RNA-seq quantiative tracks can be created for many experiments with different conditions and parameters.

The command to add the track qualifiers is, unsurprisingly:

add track_qualifier <mapSet>

For example, we can attach a qualifier "Source genome" to a track with sequence tags. Sometimes it is good to know which organism was the source for the marker sequences. We will add a corresponding qualifier to the track called "Tags":

PS> add track_qualifier "Rice-platinum standard/Os GJ-temp: IRGSP-1.0 (Nipponbare)"
Map set: Rice-platinum standard/Os GJ-temp: IRGSP-1.0 (Nipponbare)

[0] MSU gene models (Track, Order: 0, Type: Annotation)
[1] Synteny (Track, Order: 0, Type: Synteny)
[2] Gnomon gene models (Track, Order: 1, Type: Annotation)
[3] HDRA_3k_validated (Track, Order: 2, Type: GenericBp)
[4] FGENESH gene models (Track, Order: 3, Type: Annotation)
[5] Predicted TSS (Track, Order: 5, Type: GenericBp)
[6] Tags (Track, Order: 6, Type: GenericBp)
[7] Gene models (Track, Order: 7, Type: Annotation)
[8] CSHL Gene models (Track, Order: 8, Type: Annotation)
[9] Gramene Gene models (Track, Order: 9, Type: Annotation)

Select [lineNo] for the track to which the qualifier will be added: 6
Track Tags
No qualifiers found for this track
New qualifier name? Source genome
Qualifier value? IRGSP-1.0
Qualifier value has been inserted
DATA_VERSION updated

The track qualifiers can be added during loading the data. In this case, provide the qualifiers in the corresponding track section of the INI file:


; TrackQualifier: Add qualifiers that can help filtering the large track lists when using the "Edit tracks" interface in webPersephone
TrackQualifier.Tissue=Liver
TrackQualifier.Author=JHU

Use the command 'edit track_qualifier' to modify or delete the track qualifiers. Remember that when the qualifier name is changed to an empty string, the system will recognize this as a command to remove the qualifier.