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Old 02-08-2011, 10:20 AM   #1
Location: Melbourne, Australia

Join Date: Jan 2009
Posts: 37
Default Reference-guided cDNA assembly using related genomes

Dear all,

taken a look through the forum to find related questions. While there are plenty of tools for reference guided RNA-seq assembly (TopHat/Cufflinks, etc.) in general is there anything that can use the genome of a related species (at, say, 90% sequence similarity level) to guide the assembly process?

I could obviously tweak the alignment step and pass these on to an assembler, or go with a de novo assembler, just want to make sure I'm not overlooking an existing solution.

Cheers, Oliver
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