Skip to content

repeat_files.md

Latest commit

 

History

History
32 lines (26 loc) · 1.55 KB

repeat_files.md

File metadata and controls

32 lines (26 loc) · 1.55 KB

Repeat definitions

The repeat definition files are BED files containing repeat coordinates and information about the repeat structure. The first three columns specify the coordinates of the repeat region. The fourth column contains the following mandatory fields:

  • Repeat identifier (ID). The identifier must be globally unique.
  • The comma-separated list of repeat motifs (MOTIFS) specifying all possible motifs that can appear in this region. In particular, each motif present in the STRUC field must also be present in this field.
  • Repeat region structure (STRUC) field is required, although it is not currently used by TRGT. It is typically set to STRUC=<TR>. This field will be used in the future versions of the tool for defining population structure of complex repeat regions.

For example, consider this definition of tandem repeat:

chr4  3074876  3074966  ID=HTT;MOTIFS=CAG,CCG;STRUC=<TR>

It tells us that the repeat region has coordinates chr4:3074876-3074966. Its identifier is HTT. The region is expected to be composed of tandem repeats with motifs CAG and CCG.

Avoid redundant motif sets when defining repeats. For example, motifs C, ACC, and ACCAC are redundant because the sequence ACCACC can be decomposed as either ACC⋅ACC or as ACCAC⋅C. In this situation the segmentation algorithm may pick one decomposition over another simply because of the order in which motifs are listed. That makes results harder to compare across samples or runs. To avoid this issue, prefer a minimal, non-overlapping motif set.