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Old 07-29-2011, 06:35 AM   #1
tboothby
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Location: DC

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Default Finding splice variants in de novo transcriptome data

Hello,
I have recently finished assembling RNAseq data using Trinity. I am interested in finding an efficient way to identify splice variants.

All the tools I have come across do this by mapping short reads onto a reference genome (which I do not have).

Does anybody know a tool or can anyone think of a way to efficiently do this?

Cheers,
T

Last edited by tboothby; 07-29-2011 at 08:40 AM.
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Old 08-01-2011, 10:13 AM   #2
pbluescript
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You essentially do have a reference transcriptome now. You can try mapping your short reads to your assembled transcripts.
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