ChIP-Track Module

ChIP-Track is a tool that can be used to create wiggle custom tracks for data visualization through the UCSC Genome Browser.

There are two options for formatting wiggle data: variableStep and fixedStep.

variableStep format is used for data with irregular intervals between data points, and is the most popular wiggle format. The format specification is the following:

  variableStep  chrom=chrN [span=windowSize]
  chromStartA   dataValueA
  chromStartB   dataValueA
        ...  ...  

The declaration line starts with the word variableStep and is followed by the specification for a chromosome. The optional span parameter (default: span=1) allows to specifiy consecutive positions with the same data value in one single line.

fixedStep format is used for data with regular intervals between new data values and is the more compact wiggle format. The format specification is the following:

  fixedStep chrom=chrN start=position step=interval [span=windowSize]
  dataValue1
  dataValue2
  ...  

The declaration line starts with the word fixedStep and includes specifications for chromosome, start coordinate, and step size. The span specification has the same meaning as in variableStep format.

For more details on wiggle format, please refer to Wiggle Format.

 Zebrafish sample profiles of nucleosome organization around the promoter of supt6h at the dome and 256-cell stages (as displayed in Fig. 1.A, in Zhang et al., Genome Research 2014).

 CAGE-based transcriptome maps at single nucleotide resolution at the dome-30%-epiboly embryo stage of zebrafish development (Nepal et al., Genome Research 2013).

 CAGE-based transcriptome maps at single nucleotide resolution across 12 stages of zebrafish development (Nepal et al., Genome Research 2013).

 Map of Oct4, Sox2, Klf4, and c-Myc (O, S, K, and M) on the human genome during the first 48 hr of reprogramming fibroblasts to pluripotency (Soufi et al., Cell 2012). The example shows O, S, K, and M ChIP-seq profiles at gene GLIS1 (as displayed in Fig. 2.B in Soufi et al., Cell 2012).