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closeA dataset of importance to the community, but . . where is the assembly and other considerations
Posted by riano on 19 Sep 2014 at 20:13 GMT
I read with very much interest the paper by Nishiyama et al, the short read dataset will be a great resource for the sugarcane community.
But, I found it very puzzling, that the authors did not release the transcript assembly, only the underlying short reads are to be found at the NCBI's SRA. The impact of the paper will be much larger if the assembly was released. Evenmore, one can not really exploit/confirm the presented results/analysis without the transcript asembly.
I did not understand why the authors did not exploit their strand-specific short reads to directly create a strand-correct transcript assembly. I think that by mixing 454 and Ion torrent reads during the assembly some chimeras will appear (Sense - Antisense transcripts).
RE: A dataset of importance to the community, but . . where is the assembly and other considerations
glmsouza replied to riano on 29 Sep 2014 at 13:29 GMT
The ORFEome assembled sequences can be accessed at http://sucest-fun.org