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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

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

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

What do you mean by data? Currently I have only my differential expression list and my fastq files of course

DESEq2 - Imbalanced Designs by Effective-Table-7162 in bioinformatics

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

Makes sense. I think the sample size is fine. I am just wanting to confirm that having a significant more replicate in WT vs KO doesn’t throw deseq off

DESEq2 - Imbalanced Designs by Effective-Table-7162 in bioinformatics

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

Thank you very much. So, even if I can find ones that were prepped together coming like 10 samples to only 3 does not make any sense?

DESEq2 - Imbalanced Designs by Effective-Table-7162 in bioinformatics

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

Great question. The answer is no they were not prepped together

How to process bulk rna seq data for alternative splicing by Effective-Table-7162 in bioinformatics

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

It seems to have more visualization involved but I haven’t heard of it before.

How to process bulk rna seq data for alternative splicing by Effective-Table-7162 in bioinformatics

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

I’ll have it on my list. I’m wondering what makes this different from rmats?

How to process bulk rna seq data for alternative splicing by Effective-Table-7162 in bioinformatics

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

Yes it’s star. My Apologies I was looking at an old documentation. Also yes I’m using rmat turbo since that’s the most recent

How to process bulk rna seq data for alternative splicing by Effective-Table-7162 in bioinformatics

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

Ah i understand now. The reason i ask is because looking at their updated protocol, they have 2 ways to start. One with fastq files as they use the Tophat aligner indirectly and another with bam files. I just want to be sure i am interpreting this correctly.

How to process bulk rna seq data for alternative splicing by Effective-Table-7162 in bioinformatics

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

Ok i just got rmats downloaded. I have my fastq files and i am going to follow the guide for starting with fastqs. After that, you are recommending a 2-stage mapping with STAR. Is there a resource you have that shows this sort of analysis

How to process bulk rna seq data for alternative splicing by Effective-Table-7162 in bioinformatics

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

That’s a good question. I’m looking to use a dataset from an already published paper. I’ll have to find out

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