Hi All,

I am new to DESeq2 analysis and I follow the trinity pipeline for DESeq2 analysis. In that pipeline, RSEM is used to quantify the transcript abundance which generates the expected counts. These expected counts will be rounded off and later fed into DESeq2 pipeline for further analysis.

I would like to know whether these expected counts generated from RSEM can be fed into DESeq2 instead of raw counts for computing differential expressed genes?

Regards

Chudar

Yes, RSEM expected counts can be used with DESeq2.

The recommended pipeline would be to use tximport(), then DESeqDataSetFromTximport().

There is an example of importing RSEM gene-level estimated counts in the tximport vignette.

The tximport pipeline in addition to just reading in the counts table, incorporates the average transcript length per gene as a normalization factor for gene-level DE analysis. See the citation listed at the tximport landing page for more details:

https://bioconductor.org/packages/release/bioc/html/tximport.html