Resize Annotations
Resize Annotations takes an annotation track as input and outputs an annotation track with adjusted annotation lengths.
To run the tool, go to:
Tools | Utility Tools (
) | Tracks (
) | Modify Tracks (
) | Resize Annotations (
)
The following options can be configured (figure 27.23):
- Lengthen at 5' end Extend the size of the annotations at the 5' end.
- Shorten at 5' end Reduce the size of the annotations at the 5' end.
- Change 5' position by (bp) The number of basepairs by which the annotations should be lengthened or shortened.
- Lengthen at 3' end Extend the size of the annotations at the 3' end.
- Shorten at 3' end Reduce the size of the annotations at the 3' end.
- Change 3' position by (bp) The number of basepairs by which the annotations should be lengthened or shortened.
Figure 27.23: Extend all annotations by 100 bp at the 3' end.
The 5' and 3' ends are relative to the strand of the annotation. For annotations on the positive strand, the 5' end is the first position and 3' end is the last position, and vice versa for annotations on the negative strand. Annotations with no strand are treated as being on the positive strand.
An annotation corresponds to a genomic region, which can consist of a single interval, such a a gene, or multiple intervals, such as the exons of an mRNA, where each exon is depicted as a separate interval (see "mRNA" at the top of figure 27.24).
If an annotation consists of a single interval and is shortened by at least the length of that interval, it will be removed from the track (see "mRNA (shorter)" in the middle of figure 27.24).
If an annotation consists of multiple intervals, each interval is resized separately. Intervals will be removed from the annotation when the size is reduced by at least the length of the interval (see "mRNA (shorter)" in the middle of figure 27.24), and two or more intervals will be merged into a single interval if the length is increased to the point where they overlap (see "mRNA (longer)" at the bottom of figure 27.24).
Figure 27.24: A track list with three tracks. Top: an input track with two mRNA annotations - one with a single interval, the other with two intervals. Middle and bottom: the output tracks from Resize Annotations, where annotations where shortened and lengthened at the 5' end, respectively.
Extending annotations is limited to the chromosome boundaries for non-circular chromosomes. For circular chromosomes, annotations can be extended to wrap around the start or end of the chromosome.
Resized annotations that overlap (see "mRNA (longer)" at the bottom of figure 27.24) can be merged using Collapse Overlapping Annotations.