I've added linkouts to the 10X Genomics datasets as requested. I've also modified the tooltips for these datasets such that hovering over the dataset name in IGB displays the full, searchable name of the dataset in 10X Genomics.

Branch: https://bitbucket.org/pkulzer-lorainelab/quickload_scrna-seq_10xgenomics/branch/IGBF-4354

Testing by adding the following URL as a new Quickload:

• https://bitbucket.org/pkulzer-lorainelab/quickload_scrna-seq_10xgenomics/raw/IGBF-4354

Scope change request for Paige Kulzer:

Please also do the datasets that Karthik Raveendran made available for visualization in these two other genome versions:

• H_sapiens_Feb_2009
• M_musculus_Jun_2020

Ann Loraine Way ahead of you! Those changes were included with the original commit.

Sorry Paige Kulzer, I missed that!

I have a question about the dataset that appears in the Data Access Panel as "10X_MouseSplenocytes5K".

The page that opens when I click the "linkout" icon is this one:

https://www.10xgenomics.com/datasets/10k-Mouse-Neurons-3p-nextgem

The page says the dataset are neurons, but the label on the checkbox implies that these data are from spleen, not brain. I think Paige Kulzer's linkout is actually the correct one because the BAM file link URL contains words like "neuron."

Also, I see there is an issue with the way the checkbox label is crafted. This one is obviously a computer friendly way of naming a thing because it lacks spaces that in normal text indicate a separation between adjacent words.

e.g., the label is: 10X_MouseSplenocytes5k.

The more human-friendly text would be something like "10X Mouse Splenocytes 5K"

This is problematic because when IGB displays the dataset name in a track label, it "knows" to treat underscore characters like spaces and can use this to wrap text. But it can't deal with concatentated words and so has to display "MouseSplenocytes5k" as one, unbroken word.

This makes it harder to take a nice picture of this track because to make the track label readable, I have to expand the width of the track label part of the display.

I feel it would be kinder to all if we could modify the checkbox labels slightly to include spaces between adjacent words.

I've updated my branch with the above suggested changes. All track labels should now be space separated, and I've fixed the title of the Mouse dataset to reflect that neurons, not splenocytes, were used.

Ready for review!

To review the updates, I looked at the genome versions listed as supported in the Quickload's metadata field "supportedGenomeVersionInfo" and checked each data set's alignments. I also checked track metadata by selected a track label and opening the Selection Info. Doing this let me confirm that the checkbox label, its Web page and its data file URL were consistent.

The genome versions with data for this Quickload were:

S_lycopersicum_Jun_2022, M_musculus_Jun_2020, H_sapiens_Feb_2009, S_lycopersicum_Sep_2019, H_sapiens_Dec_2013

For the human genome versions, I checked alignments in the region of MEOX1, encoding a homeobox containing protein where the gene exhibits a rare exon-skipping event.
For each dataset I loaded, most of the alignments included very large gaps with flanking regions of alignment that did not match the genomic sequence at all. Not one of the ones that I checked actually matched the genome! And yet, the quality metrics reported on each data set's page on the 10X Web site typically reported very high percentages of sequences mapping to the genome.

I have just one additional request for Paige Kulzer:

• S_lycopersicum_Jun_2022 - please add a linkout to the "no max intron value" checkbox - the same as the one above it. This is just because it's not super-obvious that the two datasets are part of the same Galaxy History.

Once this last change is done, please submit a PR to Karthik's repository.

Thank you very much for making this QL site lots easier to use!

I've incorporated that requested change into my commit and raised a PR: https://bitbucket.org/KarthikRavee91/quickload_scrna-seq_10xgenomics/pull-requests/1

PR has been merged. Ann Loraine, ready for final review!

The only new change requested was adding link to a dataset offered with genome assembly S_lycopersicum_Jun_2022, also called SL5. The change is made.

To provide a kind of backup for the original repository, I forked it, and the fork is here: https://bitbucket.org/lorainelab/quickload_scrna-seq_10xgenomics/commits/branch/main

Using the bitbucket interface, I added some bitbucket-only metadata:

• repository description
• link pattern for IGB Jira project tickets

Moving to DONE!

attn:

• Karthik Raveendran
• Paige Kulzer