about transcriptome assembly

[katymeala]

Hi everyone:
I got three RNA-seq data of a species. They are sequenced in three different platforms. One is hiseq data(pair ends),one is miseq data(pair ends),the last one is hiseq data(single). I've already assembled them separately using SOAPdenovo. So now I have three assembly results corresponding to three kinds of data. And I wonder how to integrate the three assembly results together to complete a whole transcriptome, Thank you very much!

[Brian Bushnell]

I suggest you use Dedupe and/or Minimus, both of which are designed for merging multiple redundant assemblies.

[katymeala]

I suggest you use Dedupe and/or Minimus, both of which are designed for merging multiple redundant assemblies.

Hi Brian:
Thank you for your answer. As far as I know, Minimus can only merge two assemblies together while I have three assemblies. Do you have any other solutions for me?

[Brian Bushnell]

Both Dedupe and Minimus can merge any number of assemblies. I've never personally used Minimus so I don't know the exact syntax, but you should be able to simply concatenate all the assemblies together into a single file and feed that to Minimus. Dedupe is a bit easier to work with.