How to create FeatureData[Sequence] file in QIIME2

Dear All,

I have 100 pair-end fastq files. I would like to try QIIME2 otu denovo clustering. I checked the tutorial page. I need seq.fna for clustering. I tried to install QIIME1 package in my system. But due to version problems, I was not able to succeed. How can I retrieve seq.fna file from multiple pairend fastq file? is there anyway I can do it in qiime2 ?

Hi, The best way to use QIIME 1 is through Virtual Box. Its easy to install and use.

Regarding the seq.fna file, I guess you can merge multiple fastq files into single file and then convert it to ,fna file. I am not sure about this approach, maybe someone else will guide you better.

Hi @steffi!

No worries, you actually don’t need that, check out the help text for dereplicate-sequences:

  --i-sequences ARTIFACT SampleData[Sequences] |
    SampleData[SequencesWithQuality] | SampleData[JoinedSequencesWithQuality]
                          The sequences to be dereplicated.         [required]

You can provide a SampleData[SequencesWithQuality] or SampleData[JoinedSequencesWithQuality] as input. If you have paired-end reads, you can join the reads by running join-pairs.

Let us know how it goes! :qiime2:

2 Likes

Hi @thermokarst.

Thank you for the clue. It worked like a charm. But I have few doubts in dereplicate-sequences plugin. My main aim is to compare the results from OTU clustering and ASV and check which performs better. But dereplicate-sequences produce feature table indicating the number of times each amplicon sequence variant (ASV) is observed in each of my samples.

Because I did not find any differences in OTU vs ASV tables. Am I following right directions or should i run OTU clustering using qiime1?

Close! Dereplicatation doesn’t apply any denoising algorithms, so the dereplicated table is actually just the number of times the sequence was observed (not the ASV, since you aren’t working with ASVs at that step).

In general we find that ASV-based analyses agree with older OTU-based analyses, so I am not surprised to hear that. Is there something specific that you’re concerned about?