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Old 11-28-2013, 06:24 AM   #1
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Location: Brussels

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Default 454 transcriptome data

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.
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Old 11-28-2013, 10:37 AM   #2
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If you have original 454 data then try mapping those reads to the genome. This should convince you that you are looking at the right data/genome combination.

It is possible that the transcriptome assembly you have has error in it (specially if it was done 2 years ago). You may want to try reassembling the reads again.
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