About SOAP and SOAPsnp

[NicolaLosito]

Actually i have not done anything yet with CUDA but maybe i can help anyway. Just pm me or post it here that everyone else can join the discussion!

Thanks!
I made a new thread since it's a specific question ---> http://seqanswers.com/forums/showthread.php?p=71251

[sphil]

Actually i have not done anything yet with CUDA but maybe i can help anyway. Just pm me or post it here that everyone else can join the discussion!

[NicolaLosito]

@sphil: could you possibly help me with an issue I have running SOAP3 in a CUDA-4 environment? thanks!

[hus]

Oh hey sphil,

Thank you very much. I'll try that.

[sphil]

How do I sort up mapped soap files by coordinate? Is there any software I can use? Or I need to program it myself?

Hey,

on a Linux machine you can use the UNIX -sort command line option, i guess.

Don't know the paramters exactly but 'man sort' should do the job. On a Windows PC i guess you have to wirte your own script.


Best Phil

[sphil]

Err hello. sorry to interrupt here. this is my first post on this forum. i dont know to to create one.

its just that im having problem with soap2. anybody successfully run soap2? im still stuck after extracting the file. dont understand the command line options. i dont know how to start. i just want to run a sample to try out.

anybody has some sort of tutorial?

THANKS.

Hey,

give SOAP3 a try, you can find it here: http://soap.genomics.org.cn/soap3.html . It is much faster since it uses GPU power. Also there is a "tutorial" how to run it...

[hus]

Err hello. sorry to interrupt here. this is my first post on this forum. i dont know to to create one.

its just that im having problem with soap2. anybody successfully run soap2? im still stuck after extracting the file. dont understand the command line options. i dont know how to start. i just want to run a sample to try out.

anybody has some sort of tutorial?

THANKS.

[evonne16]

How do I sort up mapped soap files by coordinate? Is there any software I can use? Or I need to program it myself?