Measuring Differential Expression Using Rna-Seq In Organisms Without A Genome Or Transcriptome?"

Question

[Senthilkumar]

I have RNA-seq data from a control and experimental condition for an organism that lacks a genome and I want to measure differential expression. I have already tried doing de novo assembly of the transcriptome separately on each sample but the contigs don't match, so I don't know how to compare them. Does anyone have any suggestions for how to assess differential expression with or without assembly of the transcriptome?

Answer 1

[Brad Chapman]

Co-assemble the control and experimental results to produce a reference transcriptome. Then map the reads from each experiment onto these reference contigs and perform differential expression analysis based on these mapping results.

Answer 2

[Rm]

I liked the @Brads suggestion: Further you can look up Trinity + RSEM for differential expression of transcripts without a reference genome.