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Old 10-12-2017, 03:53 AM   #50
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Location: Belgium

Join Date: Oct 2017
Posts: 2
Default Biological question about contaminants DB

Dear Brian,

I have created a de novo transcriptome of a non-model organism. After BLASTing the contigs I found some homology with possible contaminants. My question is if I should use DNA genomes (un/masked) or the CDS gene predictions from ENSMBL database.

In the first case, do you recommend the unmasked, the masked version of genomes (ensmbl) or should I use BBMask?
And in the second case, could BBsplit handle with CDS mapping?

I am a bit lost, I think that contigs from de novo transcriptome have to be mapped against CDS sequences.

With thanks,
Microalgues is offline   Reply With Quote