Question: Differential Gene Expression Without Reference
gravatar for brontosaurus
8.1 years ago by
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 8.1 years ago by brontosaurus10

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 8.1 years ago by Steve Lianoglou5.0k
gravatar for Nicolas Rosewick
8.1 years ago by
Belgium, Brussels
Nicolas Rosewick8.8k wrote:

Try a de novo transcriptiome assembly like Trinity or Abyss.

ADD COMMENTlink written 8.1 years ago by Nicolas Rosewick8.8k
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