The data for a quantitative track like the ones above, can be loaded from bedgraph or bigWig files. Typically, such tracks show RNA-seq coverage values, levels of DNA methylation, sequence conservation, etc.

A sample control file does not have anything complex and looks like this:

[ProcessRun]
; Run ID: if specified, it uses the existing run.
;RunId=12345
; Run description: if specified, a custom description will be used. Will be ignored if a RunId is specified.
;                  otherwise, "Added quantitative data for {MapSet Accession No.} from {Sources}." will be used.
RunDescription="Added methylation profile for GRCh37.p13 from TCGA."

[MapSet]
; Either MapSetId or MapSetPath is required.
; MapSetId: id of a target map set.
;MapSetId=232287170
; MapSetPath: path of a target map set.
MapSetPath="/Human/Human GRCh37.p13"

[Quantitative]
; Source (required): a bedGraph or variable/fixed-step wiggle file located locally or remotely accessible via URL.
Source="Samples/Quantitative/jhu-usc.edu_OV.HumanMethylation27.1.lvl-3.TCGA-09-0365-01A-02D-0359-05.hg19.bedGraph"
; TrackName: track name to be displayed on the plate.
TrackName="Methylation"
; TrackDescription: track description shared across maps in the MapSet.
TrackDescription="DNA Methylation profile loaded from jhu-usc.edu"
; ElementColor: {NamedColor|HTML hex code|R,G,B}.
; ElementColor is optional, if not provided, the default Blue color will be used for positive values.
; Note, the new colors will be effective only if both ElementColor and AlternateElementColor are provided.
ElementColor=Blue
; AlternateElementColor: {NamedColor|HTML hex code|R,G,B}. AlternateElementColor is optional, if not provided, the default Red color will be used for negative values.
; Note, the new colors will be effective only if both ElementColor and AlternateElementColor are provided.
AlternateElementColor=Red

[MapMapping]
; If no mapping is found in this section, it assumes that each MAP_NAME in file exactly matches a MAP_NAME in DB.
; If map names in file are different from those in DB, map each MAP_NAME in file to its MAP_NAME, MAP_ID or ACCESION_NO in DB.
;MAP_NAME in file=MAP_NAME, MAP_ID or ACCESSION_NO in DB
1=240044684
2=240044685
3=240044686
4=240044687
5=240044688
6=240044689
7=240044690
8=240044691
9=240044692
10=240044693
11=240044694
12=240044695
13=240044696
14=240044697
15=240044698
16=240044699
17=240044700
18=240044701
19=240044702
20=240044703
21=240044704
22=240044705
X=240044706
Y=240044707

[DbSequences]
; Specific to Oracle
; The ID columns below are used in loading quantitative data.
; If there is no sequence/trigger assigned to these columns, you must specify a sequence for them.
;TABLE_NAME.COLUMN_NAME=SEQUENCE_NAME
;PROCESS_RUN.RUN_ID=ID_SEQ
;QUANT_RUN.QUANT_RUN_ID=ID_SEQ
;DESCRIPTION.DESCR_ID=ID_SEQ
;TRACK.TRACK_ID=ID_SEQ
;TRACK_STYLE.TRACK_STYLE_ID=ID_SEQ
;QUANT_RUN_PAIR.QUANT_PAIR_ID=ID_SEQ
;QUANT_RUN_QUALIFIER.QUALIFIER_ID=ID_SEQ
;QUANT_TILE.QUANT_TILE_ID=ID_SEQ



The only new things here are ElementColor (positive values) and AlternateElementColor (negative values). Note, the new colors will be effective only if both ElementColor and AlternateElementColor are provided.

The rest of the instructions follow the patterns of other INI files: the track should reference an existing map set; map names from the file can be remapped to the values from the database; etc.

In Persephone, the values in the quantitative tracks will be dynamically scaled based on either the maximum value in an entire track or in the visible portion of the track. Please check Tools/Settings/General display interface for Persephone main application:

The default value for this check box is controlled via Persephone.exe.config record:

      <setting name="DynamicallyScaleBedGraphValues" serializeAs="String">
        <value>True</value>
      </setting>

The command line

The command for adding the quantitative track is:

add quantitative -c <path to control file>

As usual, first, run it in the test mode using -t switch, then, if the tests are successful, load the data with the verbose output (-v).