When testing the 'Sam with header' file, data is successfully graphed, however, the region (chr1:1,695,935-1,696,076) that the checklist directs to is empty. Is this an issue with the data or with the testing docs? Please confirm.

Update: I tested this on IGB 9.0.2 and have observed the same thing. I have corrected the testing docs to direct to a proper range.

In the 'sequence appearance' section, deletions do not appear as a 'a gray space with a dash', but rather as shown in the deletions.png image I have attached. Is this a recent/expected change?

Update: this change was not present in IGB 9.0.2, so it must have been introduced in v9.1.0

Testing was done on macOS high sierra

https://wiki.transvar.org/display/ITD/General+Smoke+Testing and https://wiki.transvar.org/display/ITD/File+Formats seem to be redundant. Since the latter seems to be more complete, is there any reason to keep the first page around? [~aloraine]

Philip Badzuh - agreed. It is removed.

When viewing the pacBio softclipping bam, my result differs slightly from the reference screenshot. I have attached both for comparison above, Nowlan Freese.

The pacBio test file has a large number of reads stacked together. It looks like IGB is randomly sorting which reads it is showing.

One option would be to create a new test file that has a max depth of 10 reads, though I'm not sure that IGB still won't organize them differently.

I think it would suffice to make a note that the most important thing to look for when testing the pacBio file is that the left half of the reads should be soft-clipped (by default will show up as gray) and the right half of the reads will show as nucleotides or masked (blue color). If there is an issue with soft-clipping (can compare to 9.0.2) then the soft-clips will not show up at all. If there is an issue parsing the pacBio file itself (IGBF-1468) then the right part of the reads will appear as gray boxes.

Regarding Philips comment on deletions: How deletions are shown changed with soft-clipping (IGBF-1291 and IGBF-1447).

Need to update the images showing deletions in testing and in the user's guide .

The bam-pacbio smoke test file would be a good example to use for making new images, as it features soft-clips, deletions, insertions and mismatches.

I have updated the user's guide and the release testing documentation with current images of deletions.

I have updated the user's guide page linked in the previous comment with a new annotated image and have added the relevant files to the dropbox folder for this page. [~aloraine], does the page look alright?

This shows the new feature and also improves on the image that previously occupied this spot.

Additional request:

• Please copy-edit the text above the image. Check for typos, grammar problems, etc.

• Also edit for clarity if you have ideas for improvement. See Microsoft Manual of Style.

I have made some minor changes to the page for better reading and clarification.