I've updated the FindJunctions page of the User's Guide by fixing typos, creating consistent formatting between sections, and breaking up lengthy passages of text.

Questions for reviewer/Tasks still remaining:

• Are the -n and -o options optional or required?
• In the "Using FindJuctions from the command line" section, it says, "Follow the instructions to compile FindJunctions and create a "jar" file." Where are these instructions? We need to either include the instructions in the User's Guide or be more specific about where a user can find them.
• What is the difference between FindJunctions and FindJunctions (Top Hat)? We need to create some form of documentation explaining how these two differ. The only mention I can find of the latter in the User's Guide is here in the IGB Gallery: https://wiki.bioviz.org/confluence/pages/viewpage.action?pageId=852180

• -n and -o are optional as far as I know.
• Instructions for compiling should be included in the Readme for the FindJunctions repo. I would make a new ticket for adding them there.
• Would need to do some digging to determine the difference. I would assume the TopHat version uses the same logic as the junctions.bed made by TopHat.

Paige Kulzer - Apart from looking into and adding info about the TopHat version (which is separate from our version of FindJunctions, so maybe it needs its own page?), I would consider this ticket complete. Moving back to to-do so you can decide next step(s).

I've created two new tickets (see Issue Links above) to address adding compilation instructions to the FindJunctions repo and adding information about Find Junctions (Top Hat) to the user's guide.

Closing this ticket.