How to calculate the differential expression without replicate data

I am a plants.usegalaxy.eu/ user and my id is jvd.choudhary@gmail.com. I am working on miRNA differential expression, for that, I use the miRdeep2 mapper, miRdeep2 quantifier workflow and generated the quantifier tabular output, further I need to use the tool for differential expression like DeSeq2 or edgeR.

To calculate the differential expression DeSeq2 or edgeR need the replicate data. Although, I have the single set of miRNA data “control” and “treatment” without replicate. I know, replicate dataset must require for genuine calculation, but I don’t have the choice.

In plant.galaxy, I tried to use some alternative tools also, but I couldn’t get the output. From the literature support I got to know edgeR can calculate the DE from the single set of data, but plant.galaxy it couldn’t support the single set of data. So could you please enable the options of edgeR to calculate the DE or suggest some workflow to calculate the differential expression without replicate data in galaxy hub?

Hi @jvd.choudhary,

sorry, but Galaxy restricts edgeR to at least two replicates. You can find more information about this topic in the following post: DESeq2 or EdgeR or Limma without replication - #7 by jennaj

Regards