How to start with demultiplexed paired end MiSeq data analysis?

[Fred (Frederic)]

Hi everyone,
I am new in Qiime2 and I am trying to analyze my MiSeq data which is already demultiplexed. I have 40 samples, each sample has its forward.fastq.gz and reverse.fastq.gz file but I have no barcode.fastq.gz since the sequences are demultiplexed. I following the Atacama soil tutorial I assume that I should begin with the qiime dada2 denoise-paired, however I have no demux.qza file. How can I generate it?. I tried to convert my fastq.files to an artifact but it does not work:
qiime tools import
--type EMPPairedEndSequences
--input-path emp-paired-end-sequences
--output-path emp-paired-end-sequences.qza

Please, could you specify how to start with Qiime2?. Wherever I look for in the Atacama soil tutorial I realize I would need a file previously generated in Qiime and I have no clue where to begin.
Thanks a lot!!!!!

[colinbrislawn (Colin J Brislawn)]

Good morning Fred,

Because you have a pair of reads for each sample (forward and reverse), I think the fastq manifast format might be a good fit for your data. This format does not need barcodes if your reads are already split between samples.

Try processing your data set using that command, and let me know how it goes!

Colin

[Fred (Frederic)]

Hi Colin,

Many thanks for you reply. I finally got my sequences joined in the file paired-end-demux.qza. However I would like to get an idea of the quality of the sequences aligned and if any sequences have been discarded. I can not visualize any .qza file. Is it possible to conveert .qza files into .qzv?.

[thermokarst]

Hi @Fred! Glad to hear @colinbrislawn's advice got you moving forward!

You can create a visualization from of your demuxed sequences by using the demux summarize visualizer!

qiime demux summarize \
  --i-data paired-end-demux.qza \
  --o-visualization paired-end-demux.qzv

Give that a shot and let us know if you have any questions! Thanks!

[Fred (Frederic)]

Hi thermokarst!

Many thanks!!!.