Hello all,
I have a question about a transcriptome that was sequenced by Titanium 454 and assembled using Newbler's cDNA option. I'd like to do a blast search with my "unigenes" (i.e. isogroups, any contigs/isotigs not in an isogroup, and singletons). Of course, I have many more isotigs than isogroups, so it would be helpful if I could just blast the consensus sequence of an isogroup instead of blasting all the isotigs and contigs in the isogroup. Does anyone know how one might assemble all of the isotigs in an isogroup - preferably it would be an automated process so that I don't have to do it 17,000~ish times
I think the real kicker is that I don't have a reference genome for this transcriptome. Best I could do is a (relatively) closely related organism from a different genus within the family. This is going to make my head spin when I try to quantitate gene expression, so if anyone has a suggestion for mapping and quantitating a nematode transcriptome without a good reference genome I would appreciate any advice!!!
I have a question about a transcriptome that was sequenced by Titanium 454 and assembled using Newbler's cDNA option. I'd like to do a blast search with my "unigenes" (i.e. isogroups, any contigs/isotigs not in an isogroup, and singletons). Of course, I have many more isotigs than isogroups, so it would be helpful if I could just blast the consensus sequence of an isogroup instead of blasting all the isotigs and contigs in the isogroup. Does anyone know how one might assemble all of the isotigs in an isogroup - preferably it would be an automated process so that I don't have to do it 17,000~ish times
I think the real kicker is that I don't have a reference genome for this transcriptome. Best I could do is a (relatively) closely related organism from a different genus within the family. This is going to make my head spin when I try to quantitate gene expression, so if anyone has a suggestion for mapping and quantitating a nematode transcriptome without a good reference genome I would appreciate any advice!!!
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