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