Differential Gene Expression Without Reference

Question

[brontosaurus]

I have to find the differential gene expression between two genotypes of a plant species sequenced using 454 pyrosequencer.

There is no reference genome and the closest species -glycine max aligns poorly with the reads.

How does one go about DE analysis in this case?

Should i combine the reads of both genotypes, assemble them, use that as a reference genome.Then map the reads of each genotype to this reference and continue the analysis?

Thank you.

[Steve Lianoglou]

I've never done such an analysis, but depending on how different you think the two genotypes are my first crack at this would be the approach you mention: combine both datasets to assemble a transcriptome to use as a reference. Good luck!

Answer 1

[Nicolas Rosewick]

Try a de novo transcriptiome assembly like Trinity or Abyss.