Are you sure it is not working? Are you accounting for the fact that GNUMAP reports the positive strand bases, and therefore you are looking for T->C changes when you are looking for negative strand editing? I guess this depends on whether you are using .sgrex or .sam for your analysis.
If this is not the problem, then Nathan can you address this issue ASAP? I think this is the same problem we are having with our bisulfite mapping.
Thanks!
Evan
On Mar 3, 2011, at 2:44 PM, Brent Shepherd wrote:
> Hi Bryan,
>
> so it appears that the GNUMAP issue is still an issue (the minus strand part, anyway). I ran my code using the updated version, and I didn't get anything significant. So, I've reverted back to the older method and am in the process of that. That should hopefully be done by Monday. I'll keep you posted--I just wanted to give you the update.
>
> Brent