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Old 05-19-2011, 12:52 PM   #1
brachysclereid
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Default Finding Exon-Intron Junctions without a reference genome

Hi,
I'm trying to find intron-exon junctions in assembled transcriptome data without a reference genome. Does anyone know of a tool that can do this?
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Old 05-19-2011, 07:27 PM   #2
krobison
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In general this is an underdetermined problem; most of the information for making the splice lies in the introns. There is a weak signal left behind, but not much.

Your best bet is probably to compare your assembled RNA to the closest relative you can find with this information.
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Old 05-19-2011, 08:00 PM   #3
brachysclereid
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Default Finding Exon-Intron Junctions without a reference genome

Thanks for the advice. I'll try using a relative.
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Old 05-22-2011, 07:21 AM   #4
DZhang
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Hi,

You may try Cufflinks or Scripture to let the software figure out the intron/exon junctions for you.

Douglas
www.contigexpress.com
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