Avi Srivastava

Hi @WesDe , Can you try updating the ggplot2 to the latest version, reinstalling Seurat and check the data again ?

Hi @deevdevil88 , Thanks for your interest in alevin. `--keepCBFraction 1.0` should ideally be enough for a general use case to quantify _most_ of the non-junk cellular barcode however you...

Hi @sjroth , I think it's a warning (not error) with unstranded library, can you share the file `salmon-out/lib_format_counts.json` ?

Hi @AnnaAMonaco , Thanks for reaching out and I agree it'd be super useful to have alevin working for both scRNA-seq and scATAC-seq multiome datasets. In short I'd say the...

Hi @AnnaAMonaco , Thanks for clarification, I think it does makes sense to use a "reference peak set" from bulk-ATAC-seq and quantify against it. I myself am planning to use...

I guess there can be many things and it's hard to say without the logs, can you share the alevin and the salmon logs ? Like @rob-p mentioned you can...

Hi @tomsing1 , Apologies for the slow response, I was out of country for a while. Thanks for your kind words and starting a very interesting suggestion. It’s fascinating to...

Hi @xuesoso , If you have dumped the salmon's rich equivalence classes in the first round then you can run salmon in alignment mode by specifying the path of the...

Thanks @ACastanza , I think it's a good idea. I have marked it as a feature request and we'd update you here once we have some progress into the next...

Got it, thanks for the heads up. I'd probably reach out to the refgenie people about the hg38 specific versions. It makes sense to have the feature of having the...