Question: Differential Gene Expression Without Reference
1
gravatar for brontosaurus
7.1 years ago by
brontosaurus10
brontosaurus10 wrote:

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.

ADD COMMENTlink written 7.1 years ago by brontosaurus10
1

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!

ADD REPLYlink written 7.1 years ago by Steve Lianoglou5.0k
2
gravatar for Nicolas Rosewick
7.1 years ago by
Belgium, Brussels
Nicolas Rosewick7.6k wrote:

Try a de novo transcriptiome assembly like Trinity or Abyss.

ADD COMMENTlink written 7.1 years ago by Nicolas Rosewick7.6k
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