Question about importing fastq files into QIIME2


I am new to QIIME2, and I just finished the tutorials listed on the website. Now I am moving onto analyzing my own data. The first step is to import the sequencing data from the lab.

I received 3 FASTQ.gz files from the lab:

  1. Paulus_LIBR_17-19_RashmiLean2_1_S1_L001_R1_001.fastq.gz
  2. Paulus_LIBR_17-19_RashmiLean2_1_S1_L001_R2_001.fastq.gz
  3. Paulus_LIBR_17-19_RashmiLean2_1_S1_L001_I1_001.fastq.gz

I imported the first 2 files with the following command, and it did generated the “Lean2-demux-paired-end.qza” artifact.

qiime tools import --type ‘SampleData[PairedEndSequencesWithQuality]’ --input-path Lean2 --input-format CasavaOneEightSingleLanePerSampleDirFmt --output-path Lean2-demux-paired-end.qza

However, I am not sure what the 3rd file stands for. Can anyone please tell me what it is and let me know if there is anything I need to do with? Thank you!

Hi @ihl216,
It is hard to tell what that 3rd file is without knowing its content. You could simply ask your sequencing facility about the content of the data or at least post the first few of the lines from that file. It is likely that those are your barcodes which you will need to demultiplex.
Also if you haven’t already done so, have a look through this importing tutorial with regards to how different fastq formats can be imported into qiime2.

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I got back from the lab. R1 is forward, R2 is reverse and I1 is barcodes. So I assumed my data is very similar to EMP protocole so I ran the command below and created a qza file named " Lean2-emp-paired-end-sequences.qza".

qiime tools import
–type EMPPairedEndSequences
–input-path Lean2
–output-path Lean2-emp-paired-end-sequences.qza

I am hoping what I did above is correct.Thank you.

Hi @ihl216,
Great! Everything looks good to me, you'll find out soon enough if you did it correctly. If not, you'll get an error very shortly in one of your downstream steps :stuck_out_tongue:

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