Demultiplexing Help

[thermokarst]

Hi @Dean!

@Dean

I was given a .qual and .fasta file which I converted into a .fastq file and extracted the barcodes and reads

If you are going to demultiplex using the EMP protocol (demux emp-single), this is fine, but it won't work if you're planning on using q2-cutadapt's demultiplexing methods.

@Dean

q2-CasavaOneEightSingleLanePerSampleDirFmt-20xn2609/[SampleID].VSL_[Barcode]_L001_R1_001.fastq.gz is not a(n) FastqGzFormat file:

Missing sequence for record beginning on line 13

when I tried using the reads.fastq.gz (and barcodes.fastq.gz in case that worked), running cutadapt demux-single. Both times I tried running it, they returned a different SampleID and sequence for record line error.

Have you had a chance to familiarize yourself with the Importing tutorial? There are some descriptions in that tutorial that are relevant to what you are working on, and ultimately these errors come down to some fundamental mismatches between data and the commands you are trying to run on it.

@Dean

Is there a different way to extract reads from the .qual/.fasta files other than going through Q1?

Okay, so moving forward, I would recommend the following. Convert your fast+qual to fastq using whatever tool you did to accomplish that previously. Import that one fastq file as MultiplexedSingleEndBarcodeInSequence, then follow the q2-cutadapt community tutorial to demultiplex these data.

@Dean

Thanks for helping out!

No problem, that is what we are here for! Thanks for working with us to make QIIME 2 a great place to be!