u/Pristine_Temporary67

Hi guys me again. I think I have a decent understanding of the tissue to sequence process, so now I'm working to learn the analysis portion. I am mostly doing my learning through the scbest practices book and a lot of gemini.

My core question is: How necessary is it to know the different types of log normalizations like shifted normalization, scran normalization and Pearson residuals? How important is it to know the math behind it?

From my understanding, log normalization is used to account for differences in the gene expression that housekeeping genes have compared to low transcripted genes. I.E house keeping has 10k counts while gene z has only 1-5 counts. It does this by dividing the counts of gene x in cell z by the total counts in cell z then multiplying by a scale factor. Repeat this across cells and you get a list of normalized expressed values. Another question, wouldn't this be computationally intensive, if you are doing this across 20k genes and 10k cells?

Also cool news, my PI announced that I could help lead the project and potentially get a first author!!! This would be next year after their paper gets published, so I still have time. I think we will get to practice nuclei isolation in a month or two (a bit nervous but excited.)

Anyways, any help or advice would be appreciated!

- Undergrad P_T67

Hi everyone me again. I posted a while ago about learning single cell and bioinformatics. I have a question about how quality control during the analysis works. Is there some statistical tests you administer rather than just "remove samples because they contain x amount of RNA counts?" Also, for single nuclei, from my understanding the viability score is essentially flipped where now you are looking for cells alive and want that to remain lower because the cells are lysed to obtain the nuclei.

Furthermore, to verify whether your nuclei are "good" you look at the structural integrity of the nuclei through a microscope staining. My problem with that is how do you know the part you stained is representative of the large sample you have? Does a computer do it?

I will probably more in the future, so I would appreciate any advice you guys have!!

Hi so I was at a conference where I met a yale prof who said she would love to host me for next summer and we have been emailing about it.

Now I can probably get funding thru the society the conference was associated with but it probably won’t be enough as i would need rent, food, travel, etc.

How likely would it be to get accepted to the Yale Leadership SR EIP to fund the summer experience? (It would provide food, a big stipend and more than enough to cover all the costs)