Question: Protocols (workflow) for differential gene expression analysis of de novo assembled transcriptomes
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gravatar for lidanqing1990
12 months ago by
lidanqing19900 wrote:

Dear all,

I am new for bioinformatics and feel very confusing about differential gene expression analysis for de novo assembled transcriptomes. I knew Tophat +Cufflinks or HISAT+StringTie+Ballgown could be used for differential gene expression analysis for transcriptomes with reference genome. So how can I do differential gene expression analysis for de novo assembled transcriptomes? May I use the same workflow with transcriptomes with reference genome? A friend told me that I could use Bowtie + DESeq to do that, is there any other choice?

Can anyone give me suggestions? Thank you so much.

ADD COMMENTlink modified 4 months ago by predeus560 • written 12 months ago by lidanqing19900
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gravatar for predeus
4 months ago by
predeus560
Russia
predeus560 wrote:

Most of the mentioned software tools are dramatically outdated -

You have to solve one more problem than with normal differential expression analysis

Normally, you want to 1) quantify the transcripts/genes; 2) do differential expression analysis. A good quantifier is RSEM/kallisto/salmon. A good differential expression package is limma-voom/edgeR/DESeq2.

With de-novo transcripts, you have additional problem of falsely differentially expressed transcripts that actually belong to the same gene.

People suggest Corset and Lace to handle the latter problem.

ADD COMMENTlink written 4 months ago by predeus560
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