Chemical Reactivity Probing Profiles

IGV supports importing chemical reactivity probing profiles from SHAPE or MAP files. After choosing a file to import, the user will be prompted to select the applicable chromosome and optional strand and starting position. IGV will then create a .wig file (WIG format) and load it.

SHAPE format

The SHAPE format (.shape) is a tab-deliminated text file with two columns and no header.

  • 1st column: 1-based nucleotide position
  • 2nd column: chemical reactivity value, or -999 to indicate positions with no data

Example file: example.shape

MAP format

The MAP format (.map) is output by the SHAPE-MaP software pipeline ShapeMapper. The .map format is identical to the .shape format, with the addition of a third column containing standard error estimates and a fourth column containing the nucleotide sequence. These additional columns are currently ignored by IGV.

Example file: