We have generated 16S data on stool samples from mice that were exposed to high dosages of silver, using Ion Torrent PGM. I have used CLC bio to demultiplex my fastq files and also do some quality trimming. I have the filtered fasta file generated. I have a problem now. I want to use mothur for my downstream analysis. I have studied it in detail and feel like using mothur would be the best and comprehensive way to analyse the data. I am attaching one single fasta file here, extracted from one sample, on one date, on one dosage. The sequence names for these reads here are no_name and very shorter reads. I have to give it a unique name for each read? How do I combine all 16 samples in single fasta file with unique name and then run a bacth file on mothur? I am very very new to this. Please help me out here. I have a very basic data presnetation on March 12, 2013. Any help before that would be appreciated.
This is how all my data looks like and I have around 500,000 reads per sample. PLS HELP!!!