Question: differential express of RNA seq
0
gravatar for yueli7
2.2 years ago by
yueli7140
China
yueli7140 wrote:

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!

rna-seq • 729 views
ADD COMMENTlink modified 11 months ago by Biostar ♦♦ 20 • written 2.2 years ago by yueli7140

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.

ADD REPLYlink written 2.2 years ago by RamRS27k

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!

ADD REPLYlink written 2.2 years ago by yueli7140

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?

ADD REPLYlink written 2.2 years ago by RamRS27k
2
gravatar for genomax
2.2 years ago by
genomax85k
United States
genomax85k wrote:

best workflow for RNA data analysis without replications

ADD COMMENTlink written 2.2 years ago by genomax85k
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