I’m trying to quality filter and trim paired end Illumina reads.
When using the command:
qiime quality-filter q-score --i-demux S1_R1.fastq --o-filtered-sequences output/S1_R1 --o-filter-stats qoutput/S1_R1
I get this output:
ValueError: S1_R1_001.fastq is not a QIIME archive.
Am I doing this right? And can I process the forward and reverse reads at the same time?
Hi @Remon! You're supplying a FASTQ file as input and QIIME 2 is expecting an artifact (i.e. .qza file). You'll need to import your FASTQ data into an artifact (we have an importing tutorial with examples). If you haven't already, I highly recommend reviewing the Getting Started guide, which provides an introduction to QIIME 2 and links out to some tutorials for you to work through.
quality-filter q-score doesn't support processing both read directions at the same time. If you have paired-end data, we recommend joining those reads using an external program or QIIME 1's join_paired_ends.py script. You can then import the joined reads into a SampleData[SequencesWithQuality] artifact and process that with quality-filter q-score.
Note that if you're planning to use DADA2 to denoise your sequences, you'll want to avoid joining them, and using q2-quality-filter is also unnecessary. You can just let DADA2 do the joining and quality filtering for you on your paired-end data. If you're planning to use Deblur to denoise your sequences, then the strategy of joining-->import-->quality-filter-->deblur should work just fine.
We have plans to support explicit read-joining via q2-vsearch by the end of 2017, so this process may get easier in the future. We'll follow up here when that support is available in a release!
Thank you for your response, it worked!
Does the quality-filter step also remove adapters/barcodes from the sequences?
Or do I need another plugin for that?
Hey @Remon,
It does not, but typically you can use use the trim-left parameters in qiime dada2 denoise-paired to remove those pieces (since their length is known).
We've also got some plans to improve trimming/removal of non-biological sequence, so there will probably be a plugin in the near future to more directly address this.
The QIIME 2 2017.11 release has expanded support for analyzing paired end reads! See the paired end reads community tutorial for more details. 
We'll follow up here again when we have more direct support for trimming!
QIIME 2 2017.12 is now out, and it includes a cutadapt plugin! Keep your eye on the release announcement for a community tutorial on how to use the methods in this plugin!
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