I have ran mothur and uparse pipeline and they were very straightforward. now I am giving a try to qiime - but it is a headache - so un organized and not similar to what I experienced so far.

for example, I have to make a mapping file; but seems I am not pointing to the fastq file in the mapping file ?!!

In my data the reverse data quality is so bad; so I am going to use only the forward read.

so my question is how to for a mapping for for such a set up and it would be great if someone gives a hint how to "Pick OTUs through OTU table" !

Qiime mapping file example looks like

    #SampleID BarcodeSequence LinkerPrimerSequence Treatment DOB Description

I wonder which column is for the path to the fastq files ?

Also, I already have removed barcodes, primers with other tools

Thank you
QIIME is very helpful but can have it's painful moments. Here is the pipeline for the Illumina data: http://qiime.org/tutorials/processing_illumina_data.html

I make fake mapping file because I already have fastq without any adapters. Just make sure the names are correct but the sequences can be fake. Convert fastq to fasta and use the pipeline.