new user re: data import and need for demultiplexing

I am a new user and I have recently completed the moving picture tutorial as well as the gone through some of the old forum postings to see if I can get some insight to how I can go about analyzing my files. I am running into problems with importing the data.

I got my data from Illumina Miseq that was run in a multiplex setting. Each file I have received from the run can be traced back to a barcode corresponding to a sample that I used during amplicon generation. As such each sample (associated with one barcode) has two files and R1 and R2. I have a total of 18 files for the 9 samples that I wish to analyze. I think I can skip the demultiplexing step as I already have individual files. I wish to start my analysis and want to import into qiime and not sure how I can do that. Feedback or direction to where I can read more into this is much appreciated.

Take a look here:



thank you Jessy for the link. I was able to successfully use the Casava 1.8 function to demultiplex my samples. I have a quick follow up question. For my metadata file (.tsv) that I will use to generate the subsequent table.qza and qzv, does the sample IDs of (under the #q2:types column) have to match the sequencing file name exactly? i.e illumina gave me file names such as h1_S1_L001_R1_001.fastq.gz and so this is how it should appear under the column correct? otherwise I won’t be able to generate a table If I simply put h1 as my sample name in the tsv file correct?

many thanks for your input


Thanks Jessica,

I was curious would you have any resources for me better understand how to link the direction pathway to the generic name of the sample? I think I am definitely missing something cause I am just making a plain spreadsheet on google sheets and exporting it as TSV. I didnt do anything special to “link” (for lack of a better word) the generic name and the file name (which the raw data exists as R1 and R2 files for each sample) and I am not sure how to go about doing that. Thank you! you have been super helpful!


hi, I suggest you use the examples you find in this tutorial:
Use the name you already have so you won’t have any problems.

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