Completed implementing filter by samtools tags options. We can filter reads by CR number which is cell barcode number. Working on the color by option.

Color by commit: https://bitbucket.org/KarthikRavee91/karthikfork-igb/commits/771e8ab7b8a4f268bbe249a65a96aa3146703c9f
Filter by commit: https://bitbucket.org/KarthikRavee91/karthikfork-igb/commits/771e8ab7b8a4f268bbe249a65a96aa3146703c9f

During a demo showing Nowlan Freese the new filter and color options there was an error which I was not able to replicate after that. Probably someone else testing it would be better. Including the link to download installer page in my repo: https://bitbucket.org/KarthikRavee91/karthikfork-igb/downloads/

Testing Protocol

Prepare for Test:

1. Go to https://bitbucket.org/KarthikRavee91/karthikfork-igb/downloads/ and download the IGBF-3881 installer relevant to your OS
2. Install and open that IGB
3. Download the quickload folder https://drive.google.com/drive/folders/14LRo1FQ0daM0oZKZ17bo8tuW3qv0GAKk?usp=drive_link

• Add the quickload to Data Sources as " 1k A375 "
• Press Alt+P and click on the Data Sources tab
• Click on Add
• Add the path of the quickload you just downloaded
• Use " 1k A375 " as the server name

1. Click on Homo Sapiens in the carousel to load the human reference genome and click to select the track
2. Go to the annotation tab in the bottom panel of IGB
3. In the track height section, check Lock Track height and set height to 150
4. Go Data Access tab and expand 1k A375 folder on Available Data section
5. Check the only file under that folder
6. Go to the search bar on top left and search for DPH2
7. Click on Load Data and Load Sequence (top-right)
8. Right-click on one of the reads and click on Get Info
9. In the window that appears, scroll to the key "CR" and copy the value and close window

Feature Test #1

1. Right-click on the 1k A375 track and click on "Color By"
2. Click OK
3. Select Samtools Tags in Color By dropdown
4. Paste the CR value in the value text box
5. Click OK

Expected Observation: Reads with the CR value that you copied turns green and maybe some other reads as well and everything else turns red. Please check if the green ones have the same CR value as the one that you copied.

Feature Test #2

1. Right-click on the 1k A375 track and click on "Filter..."
2. Click on add button
3. Select Samtools Tags in Show only
4. Paste the CR value in the value text box and select "=" in the comparator dropdown
5. Click OK

Expected Observation: Except for the reads with the CR value that you copied, everything else disappears. Please check if the ones that remain have the same CR value as the one that you copied.

Thank you for the detailed protocol, Karthik Raveendran! This worked really well!

I walked through all of the steps outlined above and got the expected results as described for each Feature Test. I also zoomed out a bit from the DPH2 gene and made sure that the behavior I was seeing at that locus was occurring elsewhere in previously unloaded parts of the genome, too.

For reference, the CR value I was using was: ACGAAAGGTGCTTCCG
And the name of the read I initially clicked on to get that value was: A00984:1229:HTJHLDRX3:2:2137:16938:4773

Submitting a pull request on this branch is put on hold until the release branch is created for the Release IGB 10.1.0.

PR Submitted: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1047

Tested with main branch installer on Mac using Karthik's instructions above. Everything working correctly, no errors in the logs.

Closing ticket.