sequence lenght


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?



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.