I have one question related to constructing transcriptome using de novo of two genotypes for expression studies.
I have two conditions - treated and control samples - from two genotypes of a polyploid (poorly annotated) plant . I would like to do a comparative transcriptomics and identify differently regulated known/novel unigenes between two genotypes. Is it advisable to combine the unigenes from both genotypes and use this as reference for differential expression analysis and comparison between genotypes, as it is polyploidy? Or I should construct the unigenes at genotype level (by merging treated and control transcripts) and compare their expression between genotypes based on the annotation??
Please suggest and support with some references
Best
Raj
I have two conditions - treated and control samples - from two genotypes of a polyploid (poorly annotated) plant . I would like to do a comparative transcriptomics and identify differently regulated known/novel unigenes between two genotypes. Is it advisable to combine the unigenes from both genotypes and use this as reference for differential expression analysis and comparison between genotypes, as it is polyploidy? Or I should construct the unigenes at genotype level (by merging treated and control transcripts) and compare their expression between genotypes based on the annotation??
Please suggest and support with some references
Best
Raj
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