Oases; merging two Oases assembled transcriptomes

[NGSwork]

I have two independently assembled Oases transcriptome FASTA files.

Is there a way to get Oases to merge both of these assemblies into a single transcriptome FASTA file?

[RyNkA]

I have two independently assembled Oases transcriptome FASTA files.

Is there a way to get Oases to merge both of these assemblies into a single transcriptome FASTA file?

I suggest using CD-HIT-EST/TGI clustering or tr2aacds for clustering and merging assemblies. We used to yield good result using this approach.

Cheers

[bioBob]

Alternatively, why not do the merge across the two assemblies in the last step? To get to the Oases assemblies, you performed a merge across multiple kmers, perhaps you could do that same merge but across the multiple kmers from both your subassemblies.

[gringer]

I've used AMOS/minimus2 previously for two different de-novo assemblies with... results. I couldn't really evaluate the goodness of the merged assembly because the best genome assembly is still pretty bad.

[dongilbert]

See also my reply here

http://seqanswers.com/forums/showthread.php?t=40443

which is general, tested advice and software for selecting best mRNA genes from a collection of many transcript assemblies.