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Old 04-29-2012, 12:53 AM   #1
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Location: Sweden

Join Date: Jan 2012
Posts: 8
Exclamation Differential gene expression analysis without reference

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.
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