I have a 454 transcriptome dataset of a butterfly, Bicyclus. A few months ago the genome of Bicyclus was released with limited access. I tried to map some genes (from transcriptome) of my interest on the available genome using BLAST tools. However, when I BLAST genes (from transcriptome) in the Bicyclus genome dataset , I obtain a partial homology which in most cases is non-significant. What could be the possible reasons ?
For information, for the genome, the raw read coverage that went in to the assembly had a median value of around 100 X and a mean of around 200 X. However, all short reads were collapsed into long reads and then the genome was assembled using celera so essentially the coverage given to celera was much less, perhaps around 10 X. The transcriptome, on other hand was assembled de novo (two years ago) using CLC.
For information, for the genome, the raw read coverage that went in to the assembly had a median value of around 100 X and a mean of around 200 X. However, all short reads were collapsed into long reads and then the genome was assembled using celera so essentially the coverage given to celera was much less, perhaps around 10 X. The transcriptome, on other hand was assembled de novo (two years ago) using CLC.
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