Hi Nils,

Thank you for the quick response it is much appreciated! I will give it a try.

Thanks again,

On Mon, Sep 27, 2010 at 7:14 PM, Nils Homer <nilshomer@gmail.com> wrote:
Although BFAST is infinitely tunable, the masks given in the manual for human data will work well for other data (other genomes and longer reads).  The task of creating index sets also involves re-tuning the parameters within BFAST (the –K and –M options to “bfast match” and “bfast localalign”).  I would recommend sticking with the available masks,


On 9/25/10 7:01 AM, "Warren Emmett" <warren.emmett@gmail.com> wrote:

Hi there,

I have only used BFAST this far with the human genome and have since started working on zebrafish (76bp paired end Illumina) and mouse (35bp,76bp aslso Illumina). I would just like to know if there are any mask templates available (maybe I just cant find them in the manual) for these species and others? Alternatively how hard is it to create your own indexes ? It seems pretty daunting...

Thanks in advance,

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