I have ran mothur and uparse pipeline and they were very straighforward. 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 pointig 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 barcoes, primers with other tools