Concerning the demultiplex stage I have some questions about the comands input below:
qiime demux emp-single
Q1- Is there any method to demultiplex without associate to barcode (In Qiime 1.9.0 I used the multiple_split_libraries_fastq.py –i folderpairedsequence –o outputfolder –demultiplexing-method sampleid-by-file? Is there any similar command like this one?
2- What kind of file is the .qza? Is it the folder with the paired sequences? Can I just put the folder with the paired sequences as input?
3- The barcodes file is just an excel one save in .tsv? Do we need to put the barcodes and the samples name? How to transform into .fastq files? I just have them in excell.
I would greatly appreciate for any clarification.