Is HTO assay necessary for this app to be used?

[jessielyons]

Dear DALI team,

Few questions.

1. Can you please provide a link or code on how you built the seuratObj.rds object? It will help us use the app if we can reproduce your your .rds object as well and use the same for my 10x rna data too.

2. Does the DALI app really require an HTO based rnaseq data? What if we do not have this assay and it's a simple citeseq or rnaseq?

3. Do you have a version of this app where integration of vdj data is not necessary with the rna or hto data assays? Do you have a version of just vdj data that you have also created and can share?

Thanks so much,
Jessie.

[kverstae]

1. You could just follow the default Seurat pipeline to get very similar results for your 10x RNA data. An example/tutorial can be found here: https://satijalab.org/seurat/articles/pbmc3k_tutorial.html
2. HTO is not required. The example dataset we used just happened to have HTOs. Everything should just work fine with only RNA or RNA + ADT (= CITEseq)
3. I don't really see how this would work. Looking only at the VDJ data will not show you much. You wont have UMAPs/tSNEs, since these are based on your RNA/RNA + ADT. What would be the additional value of only looking at the VDJ data, ignoring the RNA and ADT?

[jessielyons]

Dali team,

OK thanks so much for your answers. I was just asking if it can be optional to have RNA data as I don't have that generated for some projects. I see your point.

Thanks again,
Jessie

[kverstae]

FYI: we got this request from other people aswell and will be looking how we can integrate this.
I will let you know when this feature is available!

[jessielyons]

Sounds great. Thanks.