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I've tested the lastest QSeq and SegMan NGen. The Segman NGen works well for both de-novo and reference guided assembly.
However, when I used Qseq and ArrayStar to profile the gene expressions in different expriments (the denovo assembly transcriptome from 454 were used as reference), an error reported in the import mapping window like "The data seems to contain no usable genes". Does it mean that Arraystar can only handle gene expression profiling in model species with genome templates? For most species, only brief annotation can be given. How to do gene expression analysis for the non-model species without genome template? Is an gene annotation process necessary before reference-guided assembly? Thanks
However, when I used Qseq and ArrayStar to profile the gene expressions in different expriments (the denovo assembly transcriptome from 454 were used as reference), an error reported in the import mapping window like "The data seems to contain no usable genes". Does it mean that Arraystar can only handle gene expression profiling in model species with genome templates? For most species, only brief annotation can be given. How to do gene expression analysis for the non-model species without genome template? Is an gene annotation process necessary before reference-guided assembly? Thanks