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  • Oases; merging two Oases assembled transcriptomes

    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?

  • #2
    Originally posted by NGSwork View Post
    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

    Comment


    • #3
      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.

      Comment


      • #4
        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.

        Comment


        • #5
          See also my reply here
          Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


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

          Comment

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