Metadata

TrackNado uses a table to turn files into well-labelled browser tracks. Each row describes one file. Columns are ordinary metadata fields that you can reuse for labels, colours, and layout.

Required and useful columns

file_path is the only required column. It contains a path to the input file. TrackNado accepts both CSV and TSV files and detects the delimiter automatically.

Column	Purpose
`file_path`	Required path to the data file.
`name`	Optional label shown in UCSC. Defaults to the file stem.
`ext`	Optional track type, such as `bigWig`, `bigBed`, or `bam`. Usually filled by `tracknado design`.
`color`	Optional colour. Use a name such as `steelblue`, a hex value such as `#4682B4`, or `R,G,B`.
other columns	Your fields, such as `assay`, `cell_type`, `condition`, and `replicate`. Use them with the grouping and colour options.

For example:

file_path,name,ext,assay,cell_type,condition,replicate,color
tracks/k562_ctcf_r1.bw,K562 CTCF rep 1,bigWig,ChIP-seq,K562,untreated,1,crimson
tracks/k562_ctcf_r2.bw,K562 CTCF rep 2,bigWig,ChIP-seq,K562,untreated,2,crimson
tracks/gm12878_ctcf_r1.bw,GM12878 CTCF rep 1,bigWig,ChIP-seq,GM12878,untreated,1,#4169E1
tracks/peaks.bb,Called peaks,bigBed,Peaks,All,,,#464646

Generate a starter table instead of typing paths by hand:

tracknado design -i tracks/*.bw -i tracks/*.bb -o tracks.csv

tracknado create --template tracks.csv creates a header-only table when that is more convenient.

Use columns when building

Pass the names of your columns—not fixed special names—to the build command:

tracknado create \
  --metadata tracks.csv \
  --output my_hub \
  --genome-name hg38 \
  --supergroup-by assay \
  --subgroup-by cell_type \
  --subgroup-by condition \
  --color-by cell_type

This makes one top-level group per assay and a cell-type-by-condition composite display within it. --color-by assigns a palette from categories. To use the explicit values in the color column instead, omit --color-by.

The color column accepts named colours (for example steelblue), six- or three-digit hex values (#4682B4 or #48B), CSS rgb(70, 130, 180), and the original comma-separated RGB form (70,130,180). TrackNado converts these to the RGB values UCSC requires.

See Organising tracks for guidance on when to use each layout option.

Derive metadata from paths

If your naming convention is consistent, TrackNado can populate fields before you edit the table. A regular expression must use named capture groups:

tracknado design \
  -i tracks/*.bw \
  -o tracks.csv \
  --grouping-regex '(?P<cell_type>[^_]+)_(?P<assay>[^_]+)'

The command adds cell_type and assay columns from names such as K562_CTCF.bw. Check the resulting rows before building: filenames are convenient input, but a metadata table is the final source of truth.

For seqnado-style directory structures, use --seqnado instead. The equivalent Python methods are .with_grouping_regex(...) and .with_metadata_extractor(tn.from_seqnado_path).

Missing group values

Blank values are acceptable if those tracks should not participate in a particular group. If every track needs a value in an active grouping field, fill the blanks in the CSV or use the Python API:

builder.with_missing_groups("Other", "condition")

This replaces empty condition values with Other before the hub is generated.