Force a Read to Align to a Specific Inverted Repeat Region
How do I force a read to align to a specific inverted repeat region?
When your reference sequence contains two or more inverted repeat elements that are longer than your ab1 trace sequences, and your ab1 traces match both repeats equally well, then SnapGene may align the read to the wrong repeat region.
This article explains how to realign individual reads with a specific repeat region.
Open the Reference Sequence
Open your reference sequence and toggle the "Show alignment" button in the side toolbar to show the "Align With" list box.
Import One or More Reads
Drag and drop reads into the List box, or alternately, use the Aligned Sequences dropdown menu to import and align your reads to the reference. The aligned read will be displayed in the Map view.
In this example, a read that is known to cover the Repeat 1 region in the forward direction, has incorrectly mapped to the inverted Repeat 2 region in the reverse direction.
There are two options to realign the read to the correct repeat.
OPTION 1: Realign a Read based on Orientation
Select the read to be realigned in the list then click Aligned Sequences → Realign Selected Sequence....
In the next dialog, check the option to "Restrict alignment to the Top Strand of the reference sequence" then click Realign.
The select read will then be realigned (if a match is found) on the specified strand. With the above settings a match can only only be found in the correct "Repeat 1" region.
OPTION 2: Realign a Read to a Selected Region of the Reference
To realign a read to a selected region of the reference follow the instructions found here: Force a Read to Align to a Specific Repeat Region
Confirm the Read has Correctly Realigned
Confirm the read has realigned to the correct repeat region of the sequence.