Hi,

I have a question about analyzing Total RNA-Seq data. The lab has generated Total RNA-Seq this time to study including lncRNAs in Inflammatory Bowel Disease. Ideally, for mRNA-Seq I usually use either EdgeR or DESeq2 based on the analysis requirements followed by customized gene enrichment and biological pathways analysis.

I usually start with the raw counts data in the mRNA-Seq, similarly the same been provided for the total RNA-Seq too. Are the processing/normalization and analysis steps of total RNA-Seq are similar to the mRNA-Seq analysis. Are there any additional customizations needed?

Thank you,

Best Regards,

Toufiq

edgeR analyses read counts. As long as you can allocate reads to genes, then the analysis pipeline is the same.