Dealing with multiple target sequences in each sample


I have 56 samples each with 4-5 amplifies genes (nifH, nosZ, nirS, nrfA, and 16S rRNA). I can use the FunGenes site for alignments after initial processing following a published article (doi:10.1038/ismej.2014.119) with amplicon sequence processing of nifH. We ran MiSeq V2 kit with 2 x 300bp. After primers, the fragments should be between ~300-560. Do I need to process the data (IE discarding and trimming) separately for each gene?

Is there any way I can do this all in mothur? I have SEED files but I don’t know how to make a reference database file for alignments.


Yes, you’ll need to process each set of sequences separately since they are not homologous.