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Hi, I've been lurking on here for a while and would now like to run something by the great wealth of knowledge that is seqanswers...
I am going to look at differential gene expression in infected vs non-infected amphibian species. I've found only a few amphibian transcriptomes and unfortunately none are closely related to my species so I am going to have to go down the de novo assembly route.
So... I have 11 individuals (5 uninfected, 6 infected) with 3 tissues = 33 samples. Having looked at my funds and spoken to experienced bioinformaticians here, I am going to run them over 4 lanes of 100bp single-end HiSeq.
Although PE reads I understand are better for de novo assembly, I've been told you can get good results with SE. Also suggested to me that I should pool all reads from all tissues and individuals to make the assembly.
So what do you think? Any comment much appreciated! (e.g. sufficient coverage for DGE etc) I've been looking at assemblers, and thought Trinity could be my best bet...but perhaps also run Abyss and Oases/Velvet and then try to merge all results into a final assembly?
Thanks for any advice!
I am going to look at differential gene expression in infected vs non-infected amphibian species. I've found only a few amphibian transcriptomes and unfortunately none are closely related to my species so I am going to have to go down the de novo assembly route.
So... I have 11 individuals (5 uninfected, 6 infected) with 3 tissues = 33 samples. Having looked at my funds and spoken to experienced bioinformaticians here, I am going to run them over 4 lanes of 100bp single-end HiSeq.
Although PE reads I understand are better for de novo assembly, I've been told you can get good results with SE. Also suggested to me that I should pool all reads from all tissues and individuals to make the assembly.
So what do you think? Any comment much appreciated! (e.g. sufficient coverage for DGE etc) I've been looking at assemblers, and thought Trinity could be my best bet...but perhaps also run Abyss and Oases/Velvet and then try to merge all results into a final assembly?
Thanks for any advice!