SOAPals, for finding splice junctions

[luke.pilling]

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

[slei]

i counter one, but do not test it.

http://biogibbs.stanford.edu/~kinfai/SpliceMap/

[feixue1039]

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

[Jon_Keats]

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).