IsoDE-bootstrap based differential gene expression analysis for RNASeq data,without replicates

Question

[mirza]

Hello, I have RNA-Seq data, without replicates for some bacteria. 1. has anyone used the IsoDE tool (http://dna.engr.uconn.edu/?page_id=517) -a bootstrap based differential gene expression analysis tool for RNASeq data,with and without replicates 2. can anyone suggest me some other tools which I can use for analysis of RNA-seq data,without replicates (other than GFOLD, edgeR, Cuffdiff,Fisher's exaact test)

Answer 1

[andrew.j.skelton73]

Firstly, no replication = bad experimental design, but there are always reasons behind that. Secondly, no replication = no statistics, you just can't infer anything when your population is 1. DESeq2 has some very conservative maths for non-replicated experiments that you can try for differential gene expression. Sleuth, part of Kallisto, might be able to handle singlet experiments for differential transcript expression, but I'm not sure.

Bottom line is that it's a bad experimental design, and you can't really perform statistics.

[mirza]

I know, one must have replicates but there are reasons. Thanks for you reply.