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Old 04-22-2010, 11:33 AM   #1
luke.pilling
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Location: Exeter

Join Date: Mar 2010
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Default SOAPals, for finding splice junctions

Hello --

I have been researching RNA-Seq and how to determine splice junctions (i.e. TopHat etc), and have just checked the SOAP website and it says they have released a new splice junction tool (18.04.2010 - so pretty recent).

http://soap.genomics.org.cn/soapals.html

However I cannot find any literature relating to it, even on their site.

I don't suppose anyone has any more information regarding SOAPals, whether it is better/worse than TopHat for anything?

Thanks for your time,

Luke
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Old 04-22-2010, 09:50 PM   #2
slei
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Default

i counter one, but do not test it.


http://biogibbs.stanford.edu/~kinfai/SpliceMap/
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Old 04-05-2011, 11:59 PM   #3
feixue1039
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Location: China

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Default

Quote:
Originally Posted by luke.pilling View Post
Hello --

I have been researching RNA-Seq and how to determine splice junctions (i.e. TopHat etc), and have just checked the SOAP website and it says they have released a new splice junction tool (18.04.2010 - so pretty recent).

http://soap.genomics.org.cn/soapals.html

However I cannot find any literature relating to it, even on their site.

I don't suppose anyone has any more information regarding SOAPals, whether it is better/worse than TopHat for anything?

Thanks for your time,

Luke
Hi, Luke

I think you can get what you want by the follow links:
http://soap.genomics.org.cn/soapsplice.html#down2

feixue1039
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Old 04-06-2011, 10:07 AM   #4
Jon_Keats
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Default

Looks like a nice application. Do you have performance comparisons using longer read lengths? And how different is it computationally (ie. speed to align 10e6 reads).
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