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.
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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