sc-RNA seq pipeline

Question

[subhiksha]

Hi all,

I am trying to analyze a single cell RNA seq data. I have two fastq files, one is before treatment and one after treatment. so ill just state my pipeline, please let me know if its right.

First I downloaded the sequences in fastq format loaded into cell ranger and using count function generated results, for both samples. using the html output, I checked for quality, everything was fine.

Now I have to use seurat for analyzing the count file that was generated and the identify deferentially expressed gene. Is it right?

[GenoMax]

subhiksha : Please validate answers on your past questions. Upvoting useful comments/accepting answers that work (green check mark) is appropriate way to show appreciation for assistance you receive on biostars.

Please read this useful book to familiarize yourself with all thing scRNA: https://bioconductor.org/books/release/OSCA/

seurat also offers useful tutorials: https://satijalab.org/seurat/articles/get_started.html

[subhiksha]

okay thank you, I am new to this community, will keep this in mind

[Ankit]

Recently I was going through some literature on Singe-cell RNA-seq and saw this https://github.com/crazyhottommy/scRNAseq-analysis-notes

May be helpful to you.

[subhiksha]

Thank you so much

[LauferVA]

you'll keep it in mind, or you will spend 5 minutes to go back and do it?

[subhiksha]

I have already upvoted the replies, people have put for my posts. I believe I am doing that right. If not please let me know.

[LauferVA]

hi subhiksha, thanks very much for following up - we appreciate it.

Here's the most important thing: Upvoting an answer is less helpful to the community than accepting a correct answer. Why? Well, actually for several key administrative reasons.

Consider any future person who has the same question that you had...now:

• Accepting an answer indicates that answer actually solves the problem. therefore, the reader can be confident that answer will work because you certified it worked for you.
• By contrast, while Upvotes are important too, they do not necessarily indicate the answer fully resolves the question. for example, some people may upvote a post that was helpful to them, but still did not definitively solve their problem. Others may use them in very different ways.
• Leaving a question open implies that no correct answer has been given. This may cause the reader to the exact question they have. But, if the question is open, they may not go to that question beacuse they assume there are no good answers there. Why this assumption? Because no answer was accepted.
• Even accepting 3 answers is fine, if all 3 are working solutions that resolve the problem.

Thanks again for writing back and asking for clarification, and for using upvotes. That already helps this community a great deal!!!!

Vincent

[subhiksha]

HI thanks for the explanation. For some reason I am not able to find the markdown accepted option in two posts of mine, including this.Kindly help regarding the same.