I’m starting to work with qiime and I have two fastq files coming from MiSeq parsing end, no barcode file. What are the steps to be able to transform it to qza and follow the analysis.
Thank you very much for your help.
I am guessing that you mean you don’t have a separate barcodes.fastq file, but do have the BarcodeSequence used inside your mapping file-right? If so, that is usually how I receive my data and barcodes are located at the beginning of my R1 and R2 fastq files. I use 12 bp golay barcodes when sequencing and these can easily be extracted and then you can follow the qiime 2 tutorial.
Hi @drmusk! The tutorials start with downloading tutorial data as an example (not everyone following the tutorials has their own data to follow along with!) — since you already have your data locally on your computer you can start with importing the results from Step 1 (extract_barcodes.py) from above.
Just for reference, we have an open issue to add support for importing this type of multiplexed sequence data, where the barcodes are contained within the sequences. We’ll follow up here when it’s available in a QIIME 2 release!