Importing reads after quality filtering

[Jo_mee]

Hello,

In the begining I want to say I am quite new to qiime2 and programming generally. I need to analyze 60 microbiome samples in Illumina pipeline, 2x250 paired end reads. The sequencing results I got in fastq.gz files. I used Trimmomatic for sequencing quality filtering. As its options predicted I obtained 4 output files: R1-paired, R2-paired, R1-unpaired, R2-unpaired. I am interested in both paired outputs.

From this moment I want to move to qiime2 to follow its analytical pipeline. I used “Moving Pictures” tutorial at first.

Importing files command:
qiime tools import
–type SampleData[PairedEndSequencesWithQuality]
–input-path FastQ/paired
–source-format CasavaOneEightSingleLanePerSampleDirFmt
–output-path FastQ-LB17_16.qza

I am not sure whether it is a correct command to import trimmed reads to artefact.
The error I got was:

There was a problem importing FastQ/paired:
_ Missing one or more files for CasavaOneEightSingleLanePerSampleDirFmt: '.+_.+_L[0-9][0-9][0-9]_R[12]001\.fastq\.gz’

Could you please suggest me any solution?
Thank you!

[Nicholas_Bokulich]

_ Missing one or more files for CasavaOneEightSingleLanePerSampleDirFmt: '.+_.+_L[0-9][0-9][0-9]_R[12] 001.fastq.gz’

Your files are not in casava8 format. A manifest format would be more appropriate, but I am really not sure what the outputs from trimmomatic are so cannot say for sure.

I would recommend just using the tools in QIIME 2 instead of trimmomatic if you wish to avoid format incompatibility: q2-cutadapt can perform the same read trimming functions, and q2-quality-filter can perform the same Q score filtering.

Good luck!