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Hi,
Im interested in finding differentially expressed genes and have come to a point where im looking for advice. Basically some of the 'most differentially expressed' genes are silenced in one species relative to the other. therefore, if one creates a de novo assembly of the species in which the gene is silenced in (anmd them maps all reads from species 1 and species 2 back to it), it wont be picked up at all even if its expressed very highly in species 2. id like to create a de novo transcriptome of one individual of each species (and maybe a third species, down the road) and then align these 2 (or 3) transcriptomes to each other to make a hybrid transcriptome. then the multiple libraries are mapped back to this. Hopefully a gene which is silenced in one species will now be present!
if anyone has any opinions or has done this please do let me know!
thanks a lot,
Im interested in finding differentially expressed genes and have come to a point where im looking for advice. Basically some of the 'most differentially expressed' genes are silenced in one species relative to the other. therefore, if one creates a de novo assembly of the species in which the gene is silenced in (anmd them maps all reads from species 1 and species 2 back to it), it wont be picked up at all even if its expressed very highly in species 2. id like to create a de novo transcriptome of one individual of each species (and maybe a third species, down the road) and then align these 2 (or 3) transcriptomes to each other to make a hybrid transcriptome. then the multiple libraries are mapped back to this. Hopefully a gene which is silenced in one species will now be present!
if anyone has any opinions or has done this please do let me know!
thanks a lot,