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  • ssaha2/ssahaET/smalt options for 454 titanium reads?

    Hi 2 all,
    I'm trying to map transcriptomic reads obtained with 454 GS FLX Titanium tecnology to a reference genome (very, usual, no big deal)
    My question is, which parameters should I use to map correctly using ssaha2 (or ssaha2EST)?, because the default parameters for 454 assumes FLX tecnology, not titanium.

    My other question is about Smalt. I found this program because one user of the MIRA maillist sugested it. It turns out that the people who did this program, are the same who did ssaha triying to fix bugs and so on, but I have the same problem: I don't know which values to put on the program options. I suppose that I should use the same, that I should use for ssaha, values which I don't know either ¿did I say that before?

    If someone can help me to solve this existential doubt, I would apreciate it.
    Help! Please.

    P.D: if I said something wrong please forgive me, my english is not very good...
    Last edited by eni; 04-07-2010, 10:15 AM.

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