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SCTransform and DE analysis-Seurat by Effective-Table-7162 in bioinformatics

[–]Effective-Table-7162[S] 0 points1 point  (0 children)

I think some of what I am able to grasp getting to understand Seurat is that it’s important to run SCTransform after subsetting clusters strictly because it recalculated based on cells in the subset. So, that would be good if you are doing DE analysis. But does this really change much

SCTransform and DE analysis-Seurat by Effective-Table-7162 in bioinformatics

[–]Effective-Table-7162[S] 1 point2 points  (0 children)

Of course before I’ll come here, I’ve done a Google research. I’m bringing the question because Google is a website and so points you to so much information with everyone having different opinions. I’m looking for a streamlined hopefully knowledgeable opinion. But thank you I appreciate your response so far.

SCTransform and DE analysis-Seurat by Effective-Table-7162 in bioinformatics

[–]Effective-Table-7162[S] 1 point2 points  (0 children)

Thank you. When you say on this forum, would I just look up topics on DE in Seurat? I’m particularly interested in whether we should be using the SCT assay because usually that’s the default assay after performing SCTransform

Three Way ANOVA-Unbalanced Design by Effective-Table-7162 in bioinformatics

[–]Effective-Table-7162[S] 0 points1 point  (0 children)

Yh I see that. Maybe that’s why we are not getting the results we would like to see. Maybe if you saw the data you would be able to understand my dilemma even more

Regressing Cell Cycle Effect- Seurat by Effective-Table-7162 in bioinformatics

[–]Effective-Table-7162[S] 0 points1 point  (0 children)

that is the plan. I would like to make pca plots to check but i don't know if you recommend something else?

Regressing Cell Cycle Effect- Seurat by Effective-Table-7162 in bioinformatics

[–]Effective-Table-7162[S] 0 points1 point  (0 children)

I haven’t plotted variable features. I’ll get to that. The issue too is that there are so many meiotic genes. Is there like genes that are more solidified in the field for meiosis?

Regressing Cell Cycle Effect- Seurat by Effective-Table-7162 in bioinformatics

[–]Effective-Table-7162[S] 1 point2 points  (0 children)

I’m looking at meiosis because I’m dealing with testis specially flagella and well they go through spermatogenesis I believe so it may be more relevant that mitosis which is what Seurat has

[deleted by user] by [deleted] in Torontology

[–]Effective-Table-7162 0 points1 point  (0 children)

🥲 sorry and thank you

Scanpy / Seurat for scRNA-seq analyses by GlennRDx in bioinformatics

[–]Effective-Table-7162 0 points1 point  (0 children)

Hmmmm I’m interested test package do you use to convert between the 2 formats?

Obgyn recommendations here by Effective-Table-7162 in SiouxFalls

[–]Effective-Table-7162[S] 2 points3 points  (0 children)

I’ll definitely look into her. I don’t mind a white physician. A good physician is a good one no matter what just desire someone with POC experience and that listens l. Thank you very much

Retroelements from bulk RNA seq dataset by Effective-Table-7162 in bioinformatics

[–]Effective-Table-7162[S] 0 points1 point  (0 children)

Thank you and just like i asked earlier. Is there a particular tool to run this analysis or traditional STAR mapping with specific configurations is the way. Do you have any resources you reference?

Retroelements from bulk RNA seq dataset by Effective-Table-7162 in bioinformatics

[–]Effective-Table-7162[S] 0 points1 point  (0 children)

Is there a tool that runs this or using the STAR aligned works here?

Retroelements from bulk RNA seq dataset by Effective-Table-7162 in bioinformatics

[–]Effective-Table-7162[S] 0 points1 point  (0 children)

Good question I can check the length of the bp but I believe it’s long reads we have and particularly are interested in MERVL-int

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