<p>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?</p>

<p>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.</p>
