File formats

Track data (.csv)

Track data can be added to a project through csv files. Metadata is provided to the workflow to find a column of values in that file. The data in that column is required to be a number, and is converted to float values when it is read in.

The workflow requires:

  1. The csv file’s first line will define column names.

  2. The file must have at least column. There is no limit on the number of columns in a file.

  3. A column that is called out as having track values shall have float values.

  4. There must be at least as many values in a track column as there are beads in the project.

The simplest track file will look something like this, which contains values for a track named ‘velocity’:

velocity
1.0
3.0
9.0
...

Features file (.csv)

A features file is a csv file that describes a feature in a DNA sequence. These can be included in a project so that a user can define portions of the sequence that can be easily selected with the 4D Genome Browser UI. The data fields are meant to capture the data that can be extracted from a gff file. In particular, the id, type, and name fields are values that are parsed from the attributes value in a gff file.

  • name: a meaningful string. Equivalent to the Name gff field.

  • start: the start position of the feature.

  • end: the end position of the feature.

  • id: a unique identifier for the feature. Equivalent to the ID gff field.

  • type: the type of feature. Typically a feature type found in gff files, but any string can be used. Equivalent to the biotype gff field.

name,start,end,id,type
some_name,200000,400000,firsthalf,feature
some_gene,600000,800000,some_gene,gene
...