Miseq pair-end fastq data

I am new on QIIME 2 and not sure how to make the barcode table or/and metadata table, since the sequencing data that we have from Miseq is demultiplexed pair-end, each sample has two files with read1 and read2. The barcodes has been removed in the fastq files. I have looked at the tutorial and found that the demo Casava 1.8 paired-end demultiplexed fastq is close our fastq format, however, by following it I can only generate demux-paired-end.qza as output artifast, then I am not sure what is next step. I tried back to follow picturing moving, but don’t know how to generate a barcode or metadata table. Could you please let us how to do it. Thank you.

1 Like

Hi @jli! Since your data are already demultiplexed, you can skip that step of the Moving Pictures tutorial. Using qiime demux emp-single or qiime demux emp-paired is only necessary if your data are multiplexed.

Once you have your demultiplexed paired-end sequences imported, you can use qiime demux summarize to inspect the imported data and make sure it looks right. There are also interactive quality score plots that will be useful in determining the parameters to use with DADA2, which is typically the next step in your analysis (Deblur is also an option).

Once you have imported your demux data and inspected it with qiime demux summarize, you can pick up at the denoising step of the Moving Pictures tutorial. Note that since you have paired-end data, the commands will be different (you’ll want to use qiime dada2 denoise-paired instead of qiime dada2 denoise-single). For examples of analyzing paired-end data, check out the Atacama soils tutorial (note: you can also skip the demultiplexing step in the Atacama soils tutorial because your data are already demultiplexed).

Let us know how it goes!

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.