hi
i am working on a rna seq dataset which was sequenced PE with 454 and Hiseq. I have assembled 454 with newbler and hiseq using trinity. There is no reference available for the animal which i am working. So i wanted to construct a reference transcriptome using this information. We have lot of coverage more than 30X atleast. What is the best way to use this information to construct reference trascriptome ?
so far with my searching MIRA performs this hybrid assembly but it takes reads and do the assembly. I have the assembled transcripts and i need a pipeline of things i can do to use already assembled transcripts from illumina and 454 and built the reference.
I would like to know how to do meta assembly by using the assemblies through Trinity and newbler of Roche transcriptome data. I used CAP3 so I followed the following commands. Both files have different headers and parameters.
Output: .contigs, .singlets, .ace. links
I think
.contigs
are assembled and.singlets
are unassembled data. Here I don't have.con
file as well as I am unable to generate by formcon.Please guide me how can I get more assembled contigs . Please guide what will be the right way to do.Can you please guide me how the make mira's input to generate meta assembly.