Importing demultiplexed fastq files from torrent

[Imindias (Isabel Moreno-Indias)]

Hi!
I am finally changing into qiime2 and I am having some problems with the importation of the data.
I have fastq files from the Ion S5 sequencer. I am trying to use the Casava 1.8 single-end demultiplexed fastq example with QIIME2 studio, but this error emerged:
BAD REQUEST - Missing one or more files for CasavaOneEightSingleLanePerSampleDirFmt: '.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz’
but my sequences are in a normal format: 1_10.fastq that in quiime1 works.
I have compressed it to 1_10.fastq.gz before, but the error emerged.
I know this example is for illumina sequences, but this was the most similar example I have seen to follow.
Could you help me, please?
thanks in advance
Isabel

[thermokarst]

Hi @Imindias!

The Casava formats are specifically for Illumina sequencing products, which won’t work with your ion torrent data without some manipulation. Instead of using a Casava format for importing into QIIME 2, I would suggest using one of our fastq manifest formats — please take a look at the linked docs for more details. Importing your data is probably the hardest part — once it is in a QIIME 2 artifact, you should be able to follow along with any of the tutorials, making minor adjustments for your particular analysis!

As well, we don’t officially support ion torrent data, but in theory you should be able to process it with q2-dada2, specifying a trim-left value of 15 (see the DADA2 docs for details). Let us know how it works for you!

Thanks!