Created a new page for Filter: https://wiki.transvar.org/display/igbman/Filter+annotation+data

Recommendations:

• Change first sentence to explain what is meant by "filter". Users need to know what this feature actually does right off the bat so that they will know whether they need to keep reading or move on to another page to find the functionality they are looking for. Filtering in this context means: hiding or showing things based on their attributes, such as whether or not reads have gaps. This first sentence is the "lede" which ought to summarize in a descriptive way what the feature is doing and why it could be useful. But of course, it needs to also be brief.

• The image helps and is great, but it is also a bit confusing because a new user might see this and have no idea what they are looking at. Explanatory call-outs and a legend could help a ton. I would recommend making a figure containing two images - one with filtering turned on and another with filtering turned off. Call-outs can point out the filter mark, which is otherwise very cryptic.

• When showing images in the user's guide, I would like for us to explain to readers how they can reproduce the image. To do this, let's create figure legends that have a two-part structure: First part explains what the image is showing and the second part explains how the image was created, using language reminiscent of the figure legend from a well-written research article.

• The callout lines point out components of the interface in the later figures are a lot thicker than on other pages. Also there is a thicker black border around the images that does not appear for images on other pages. It would be good to have a consistent appearance throughout the user's guide.

• If you have not already done so, do please add the content to the Dropbox folder "IGB Users Guide Art and Style info"

I changed the first sentence based on the above recommendation.

I added a before filtered image.

I added a section on how to reproduce the top images.

I reformatted all of the images so that they would be more consistent.

Two issues:
I created an image with figure legends that described how to replicate the image. However, I found it to be not as useful as a full description. I could not find a way to add a figure legend within confluence so I tried adding the figure legend as part of the image itself. However, this meant that the text could not be copied or searched, which I found undesirable.

I do not have access to the Dropbox folder "IGB Users Guide Art and Style info" through the Loraine Lab UNCC (lorainelabuncc@gmail.com) Dropbox account. When I click on this link it informs me that I need to add it to my Dropbox account and ask for access. I think it would be much easier if we created a Google Drive folder for the User's Guide. This would make it easier to control who has access and we can use the Google Slides to directly create figures. We can then include the link to the specific slide in the Jira issue.

Powerpoint slides with images has been placed in the Dropbox folder "IGB Users Guide Art and Style info".