[maker-devel] Transcriptome Assmeblies for Protein Evidence

[Carson Holt]

You should use the scaffolds.  Large gaps will not affect the annotation
and are common in the scaffolds of all newly assembled genomes.

Thanks,
Carson


On 1/27/14, 9:17 AM, "Li, Michael" <Michael.Li3 at AGR.GC.CA> wrote:

>Hi everyone,
>
>I've been tasked to run MAKER on a genome that we have recently sequenced
>and assembled de novo. Along with the genome, the transcriptome has also
>been assembled using SOAPdenovo. I've been told that we've experimented
>with different kmers, but I'm not sure which kmer is ideal for use.
>
>One kmer assembly has the highest N50 for contigs, while another has the
>highest N50 for scaffolds, but it comes with a lot of gaps.
>
>Would gaps impact how MAKER handles evidence alignment or the overall
>annotation? Or would either work well with MAKER?
>
>Thanks in advance!
>
>Michael Li
>Co-op Student
>
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