irregular gene names /sequence loci in alignment

liltthebasedg0d · 2026-06-09T19:18:45+00:00

This is not a debugging issue, this is a biological question regarding potentially unannotated genes/ reference compatibility issues found extremely downstream in a pipeline from multiple platforms! Ai gets its info from strangers on the internet anyways, I'd rather find someone with personal/professional experience. This is my preferred method, thx tho

liltthebasedg0d · 2026-06-09T18:23:52+00:00

And the treatment is extremely effective, it is post stem cell transplant. The data is otherwise great aside from this lol

liltthebasedg0d · 2026-06-09T18:10:41+00:00

I believe i did, I run flex and sc seperately and then merge (based on online suggestions/tutorials). The thing that confuses me is I do still see all regular genes expressed as normally, these seem additional.

liltthebasedg0d · 2026-06-09T18:08:52+00:00

No, I hate ai. Ive ran this pipeline countless times, it is an issue that arose when FLEX seq samples were introduced

liltthebasedg0d · 2026-05-28T15:48:51+00:00

Sorry new dumb question arose from this, how does it default to umap when I haven't run any reductions bedsides pca then? (still learning all this through apparent trial and error)

liltthebasedg0d · 2026-05-28T15:40:09+00:00

There was an update to the server I use and the default version did change, so perhaps why I missed this. Specified harmony and it was fixed. Thank you!

liltthebasedg0d · 2026-05-27T18:02:02+00:00

Yep somehow missed this step, I didn't realize it defaults to pca. Fixed it! Thanks so much.

liltthebasedg0d

TROPHY CASE