.fq sequence files import

Hi! I have .fq sequence files of several samples from Illumina 1.9, an example file of one sample is here

. Please help me on how to import all the sample .fq files into QIIME2 for downstream analysis. I am using QIIME2 version 2017.10. Thanks!

Hi @bsen2018!

It looks like these are merged fastq files? If so you should update to QIIME 2 2017.12 (2017.11 technically added support for merged/joined reads).

Otherwise, I would check out the Importing Tutorial. You can either go with a manifest file route, where you create a row for every fastq file. Or if you have the raw fastq files with Casava’s standard naming convention, you can import an entire directory.

Let me know if you need more info!

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Thanks for suggestions. As I am not an expert in working on a command line, I am unable to follow exactly the manifest file route. The file naming convention that sequencing company has provided does not follow the Cassava1.8. Is it possible to update QIIME2 from the command line or I should download the whole core distribution package (QIIME2 2017.12) and replace it with the older version that is currently installed in my pc? I have the forward and reverse paired end read files of each sample too. Please let me know what is the best solution. Thanks!


I tried to make the manifest file and then followed the command in QIIME2 2017.10. I get the following error

. Here are the R1 and R2 read files. Please let me know how to resolve this. Am I going wrong somewhere? Thanks!


Hi @bsen2018!

Yes, the only exception will be the q2studio application icon will keep using the old version (2017.10), but it doesn’t look like that will be an issue for you. Check out this post for some instructions.

Do you plan on doing any analysis with DADA2? If so we want to use those directly (forward and reverse are denoised independently before being merged). Otherwise there’s no problem starting with your merged sequences.

It does look like you have the paired-end sequences more or less sorted out though, so I would use those since you have them.

The --type argument just needs to be swapped from SampleData[SequencesWithQuality] to SampleData[PairedEndSequencesWithQuality] otherwise what you have looks great!

Let me know if you run into further issues!

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With your suggestions, I have now successfully imported the .fq files and the downstream processing worked. I am now attempting to update the QIIME 2 release from command line. Hope it works.Thanks!


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