First noticed with in version 8.2.0:

User story:

The Find Junctions feature lets a user created so-called "junction features" in a new track using a BAM (alignments) track as input.
To use the feature, a user:

• loads a BAM track
• right-clicks the BAM track's track label
• selects Tracks Operations
• selects Find Junctions or Find Junctions (Tophat)

(These are just two different ways to calculate a junction feature).

When the user selects a Find Junctions operation, a new window appears with settings for the operation. One of the setting is poorly labeled and likely does not make sense to a new user. This needs to be fixed. For "Find Junctions" the setting is called "flank" and for "Find Junctions (Tophat)" the setting is labeled "threshold". They have the same effect and the description should be the same.

What they mean: This setting determines the minimum number of bases that need to align across a junction on either side in order for a split read to be used to create a junction feature. The fact that the track that is made has blocks that are the threshold size helps make this apparent, but it would be really good to have a tool tip, or optional info button or something to help the user figure out what the threshold option does.

Task:

• Investigate whether or not we can change this labeling, and how to do it. To be more informative, the label should read:
• Add a comment making note of files and modules that would need to be edited.
• Make the change as required, if feasible.

"Enter minimum number of bases required to align on each side of the intron/junction:"

Note: Consult with Dr. Freese if you have questions about how to proceed.

Caution: All Track Operations are using the same UI code. Watch out!