Question: DEGs from *genes.results or *isoforms.results
1
gravatar for Bioin
4 weeks ago by
Bioin10
Bioin10 wrote:

Hi Biostars,

I got two output files (*genes.results and *isoforms.results) from aligning reads to the Trinity denovo assembly(Trinity.fasta) with Bowtie2 and expected read counts with RSEM. Out of two output files, which one should I feed to DESeq2 for identifying DEGs.

Any suggestions will be appreciated. Thanks in advance.

rna-seq alignment assembly • 118 views
ADD COMMENTlink modified 29 days ago • written 4 weeks ago by Bioin10
3
gravatar for JC
4 weeks ago by
JC9.1k
Mexico
JC9.1k wrote:

Depends on what do you really want, the genes table represents the global expression of the gene (as a summary of all isoforms for the gene), the isoforms table is for each transcript of the gene. So, if you run DESeq2 in genes, you get genes, and isoforms, you get transcripts.

From a biological point of view, genes are representing a general function, the isoforms a more controlled regulation, if the biological response is to shut down the gene, you can expect all isoforms will be downregulated, but if the biological response requires to shut down a particular isoform, the gene will be not DE, but one isoform will be.

ADD COMMENTlink written 4 weeks ago by JC9.1k
1
gravatar for Bioin
29 days ago by
Bioin10
Bioin10 wrote:

That means if I want gene level LFC I need to input *genes.results and for transcript level LFC *isoforms.results file should be used. Thank you.

ADD COMMENTlink modified 29 days ago • written 29 days ago by Bioin10
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