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

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?

non differential rna
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updated by Biostar Biostar • written by Senthilkumar • Senthilkumar

Brad, you may like to post this as an answer.

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written by Michael Dondrup Michael Dondrup

2 answers

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.

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written by Brad Chapman Brad Chapman

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

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written by Rm Rm

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