differential express of RNA seq

Question

[yueli7]

Hello,

This is my first time analysis RNA seq data.

I have already used STAR, featureCounts. Then, I will try to find the differential expressed genes.

Which software is suitable for human, and no duplicate RNA seq data?

Thanks in advance!

[Ram]

I'd recommend you get the Biostar Handbook, as it is a complete guide to learning various aspects of bioinformatics; especially relevant to you would be the recently added section on RNA-seq.

[yueli7]

Thank you for your reply.

A paper published in BMC Bioinformatics "Evaluation of methods for differential expression analysis on multi-group RNA-seq count data" mentioned: for data without replicates, the DEGES-based pipeline with DESeq2 can be recommended.

Thus, I really confused about which software has the best performance: edggeR, GFOLD or DESeq2?

Thank you!

[Ram]

Quick question. You said:

This is my first time analysis RNA seq data.

This post of yours from 3 years ago is on RNA seq: differenrially expressed mRNA pvalue FRD

Those two statements contradict each other. Which of these is accurate please?

Answer 1

[GenoMax]

best workflow for RNA data analysis without replications