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Re: SSAHA2 setup to search for primer binding sites

Hi Adam, Thanks for the quick response. Do you have any idea of the amount of memory neccessary to build the hashtable of the Human genomic sequence? I am
Oct 17, 2007

Re: SSAHA2 setup to search for primer binding sites

Hi, To hit short reads allowing mis-matches you will need to use -skip 1, kmer 12 is usually fine. Cheers. -- Dr Adam Spargo High Performance Assembly Group
Adam Spargo
Oct 12, 2007

SSAHA2 setup to search for primer binding sites

Hi, I am trying to setup SSAHA2 to search for primer binding sites in the human genome. The app we currently have that does this uses BLAST, but I would like
Oct 11, 2007

Re: Error running latest ssaha

... Having looked at this some more I found that if you use a full path to specify the location of the fasta file when you create the hash initially you can
Aug 24, 2007

Re: Error running latest ssaha

You're right, there does seem to be an issue when you specify '-sf hash' - both query and subject need to be in the same directory. Interestingly it always
Aug 23, 2007

Re: Error running latest ssaha

... Tony, Thanks for the reply. I've checked, and test.fa is definitely using unix line endings already. Having played with this a bit more it seems this is
Aug 23, 2007

Re: Error running latest ssaha

Hi Your command should work if test.fa is in valid fasta format. However the file needs to be in UNIX text file format - ie just one character at each
Aug 23, 2007

Error running latest ssaha

I'm trying to run ssaha on a fedora 7 (32bit) system and it's dying with an error every time I run it. I'm running the latest v33 version of ssaha, but I've
Aug 23, 2007

Re: ssaha2 v1.0.4

... Dear Tony, many thanks! I will announce on this mailing list when the Debian package will be ready. Have a nice day, -- Charles Plessy
Charles Plessy
May 19, 2007

Re: ssaha2 v1.0.4

Dear Charles/Adam I have made the changes necessary to get 'original' SSAHA to compile under gcc 4.1.2 and uploaded a new version of the package to this group
May 18, 2007

New file uploaded to ssahausers

Hello, This email message is a notification to let you know that a file has been uploaded to the Files area of the ssahausers group. File :
May 18, 2007

Re: ssaha2 v1.0.4

... Dear Adam, there is a major difference between SSAHA and SSAHA2: the first is free software, and unfortunately the second is not. I would be happy to
Charles Plessy
May 5, 2007

ssaha2 v1.0.4

Hi, Sorry if I haven't replied to resent requests in person, all reported issues should be solved by this new release:
Adam Spargo
May 4, 2007

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Apr 9, 2007


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Mar 30, 2007
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