Here is a series command with detailed explanation for my last analysis of 16s RNA gene from illumina hi-seqs
Could be useful for to follow
http://shuixia100.weebly.com/1/post/2011/12/mothur-tutorial-1.html
General introduction of Mothur analysis:
http://shuixia100.weebly.com/1/post/2011/12/mothur-tutorial-2_analysis-example.html
1.Generate fasta and qual file from fastq
2.make oligos and trim seqs
3.use unique.seqs to get rid of the repeated sequences in your dataset.
http://shuixia100.weebly.com/1/post/2011/12/mothur-tutorial-3_analysis-example.html
1.align your seqs against a given template
2.filter out the columns only contains gap from your align result
3. generate dist matrix from your sequences
4. Cluster your seqs into OTUs
http://shuixia100.weebly.com/1/post/2011/12/mothur-tutorial-4_analysis-example1.html
1 find the OTU abundance among your samples by make.shared
2 further transpose the make.shared result to get a matrix use to draw heatmap
http://shuixia100.weebly.com/1/post/2011/12/mothur-tutorial-4_analysis-example.htm
1.assign classification to all of your seqs
2.assign classification to your OTUs based from the shared file and classification of your seqs