very naive question on fasta file

Hi
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!!!

No_name
TCCACGC
No_name
TCCACGCCGTAAACGATGATCACTAGGTGTCGGTGGGCATGGGCATCGGTGCCGCAGAAA
CGCAATAAG
No_name
TCCACGCCGTAAACGATGAGTACTAGCTGTCGGAGGTTACCCCTTCGGTGCGCAGCTAAC
GCATTAAGTACTCCGCC
No_name
TCCAC
No_name
TCCACGCCGTAAACGATGAGTACTAGCTGTCGGAGTTACCCCTTCGTGGCGCAGCTAACG
CATTAAGTACTCGCCTGGGAAGTACGCTCGCAAGAGATGAACTCAAGGAATTGGACGGGC
CCGCACAAGA
No_name
TCCACACAGTAAACGATGAATACTCGCTGTTGCGATATACAGTAGCGGCCAAGCGAAAGC
GTTAAGTATTC
No_name
TCCACGCCGTAAACGATGAATACTAGGTACAGGGGCACAAAAAGTGCTTTCTGTGCCGCA
GCTAACGCAATAAGTATTCCACCTGGGGAGTACGTTCGCAAGAATGAAACTCAAAGGAAT
TGACGGGGCCCGCACAAGGA
No_name
TCCACAC
No_name
TCCACGCCGTAAACGATGAATACTAGGTAC
No_name
TCC
No_name
TCCACGCTGTAAACGATCAATACTAGGTGTGCGGGGACTGACCCCCTGCGTGCCGGAGTT
AACACAATAAGTATTGCACCTGGGGAGTACGATCGCAAGGTTGAAACTCAAAGGAATTGA
CGGGGCCCGGCCACA
No_name
TCCACGCCGTAAACGATGAATACTAGGTGTAGGGGTTGTCATGACCTCTGTGCCGCCGCT
AACGCATTAAGTATTCCGTCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGA
CGGGGGCCCGCACAAGA

Padmini
FDA

The problem is likely with CLC bio. Why not use mothur for these steps? For what its worth, we have been seeing very high error rates with IT data that makes me wonder whether it’s usable for 16S stuff. We hope to have a IT pipeline by the end of the month.

Pat