How to visualize scRNA-seq normalized data

Question

[SlowSD]

Hello there,

I am new to single cell RNA sequence analysis and have lot of doubts. The principle doubt I have is regarding normalization of data.

How I can I visualize the normalized data?

This YouTube video Normalization methods for single cell RNA-seq data explain the concept of normalization very well. But upon performing normalization, I didn't see any change in my data for e.g the summary, nCount_RNA, and nFeature_RNA values remain the same.

How can I plot the transcript detected vs cell index plot mentioned in the Youtube video?

Thank you.

Answer 1

[ATpoint]

I am new to single cell RNA sequence analysis and have lot of doubts.

My suggestion is to follow guided tutorials. Three big ones in this are:

• Bioconductor ecosystem: https://bioconductor.org/books/release/OSCA/ (my recommendation!)
• Seurat ecosystem: https://satijalab.org/seurat/articles/get_started_v5_new
• ScanPy / Python ecosystem: https://scanpy.readthedocs.io/en/stable/tutorials.html

and more generally: https://www.sc-best-practices.org/preamble.html

Don't try and learn everything yourself, and with the help of random videos. Follow the "official" sources first.

But upon performing normalization, I didn't see any change in my data for e.g the summary, nCount_RNA, and nFeature_RNA values remain the same.

Of course. nCount_RNA is the raw number of reads per cell, "raw" does not change upon normalization. nFeature_RNA is the number of genes detected with at least one counts, so that is independent of normalization as well.

Please spend some quality days with above resources, explore your data.

[SlowSD]

Thank you for reply.

You are right. I should spend time reading the documentations. However, after each step of processing, I want to visualize what has changed.

After the log normalization, how can I see the normalized values?

I will surely try to learn from official documentations.

Thanks