orientation

This function performs strand assignment of an unassigned feature based on another overlapping feature, thereby enabling the strand asymmetry analysis of the first.

Required inputs:

Argument	Explanation
motif_no_annotation	Un-annotated file to which strand assignment will be added.
motif_annotation	Strand-annotated file used to extract strand annotation from.

Output:

• Un-annotated BED formatted motif with annotation based on motif_annotation file.

Note

In the case of multiple overlaps, we assign the sign of the annotated region whose center is the closest to the center of the un-annotated region.