sequence lenght

Hi,

i am new Mothur user.
i have a question about sequence lenght.
My sequences are 16S rRNA clones (sequenced with M13 forvard primer). I made a chimera chek with bellerophon from greengens and i also process them in DNA Baser. After that, when opening them in MEGA5 program i saw that some of them have different orientation (some started with 27F bacterial primer, others don not). So i kept the ones that started with 27F , and made a reverse compement on the others. Then i aligned them with MUSLE (MEGA5) but after that i had very long ends on both sides and rather short overlap. Should i treem them before processing them in mothur?

thanks,

maj_cika

Why not just process them all the way in mothur? Although some of the initial steps are different for 454 and Sanger, the SOP would be a good place to start to see where your data can figure in. Eventually, everything does need to be trimmed to the same alignment coordinates.