Single cell analysis

Question

[leticia]

Hello, I am new to single cell analysis and i wanna know if we can perfom a single cell analysis from RNA seq database downloaded from TCGA cbioportal ? How can we set our counts matrix if so ? Please can anybody give me a clear explanation about it ? I have already search in many articles and tutorials but i didn't find the answer to my question so please can you help me ?

Answer 1

[Kevin Blighe]

Hi, which data, specifically, have you downloaded? If you can provide a direct link to the file(s), that would be good.

[leticia]

This is the type of data i downloaded : mRNA expression z-scores relative to diploid samples (RNA Seq V2 RSEM) Breast Invasive Carcinoma (TCGA, PanCancer Atlas) , but i don't know how to use it for single cell analysis.

[leticia]

[Kevin Blighe]

Hi, that is not single-cell data. That is bulk RNA-seq via RSEM. Please read the FAQ at cBioPortal: https://docs.cbioportal.org/1.-general/faq#how-is-tcga-rnaseqv2-processed-what-units-are-used

How is TCGA RNASeqV2 processed? What units are used? RNASeqV2 from TCGA is processed and normalized using RSEM. Specifically, the RNASeq V2 data in cBioPortal corresponds to the rsem.genes.normalized_results file from TCGA. A more detailed explanation of RSEM output can be found here. cBioPortal then calculates z-scores as described above in What are mRNA and microRNA Z-Scores?

If you need single-cell data, then you could search GEO. There are many single-cell datasets there, and the raw counts are usually available.

[leticia]

Thanks a lot for your help , it's clear for me now.