I have received some data from Mr. DNA. They have given me 2 fastq files that have 20 simples combined into the 2 fastq files (read 1 and read 2). Is there a straightforward way of importing these into QIIME 2? There website recommended joining the fastq’s into 1 file using the join_paired_ends.py script from QIIME 1 and then running it through there fastq processor which spits out a barcodes.fastq, reads.fastq, and a non-barcodes.fastq, and then running it through split_libraries_fastq. I did all of this and generated a seqs.fna but I am not sure that is the best approach. Any thoughts?
Relevant forum posts... I mention that, because (as I understand it), Mr DNA substitutes the barcodes after sequencing, replacing them with what is essentially placeholder nucleotides. With all that said, you should also have received a file that identifies which barcode belongs to which sample. If you have that, you can import and demux using q2-cutadapt! Check out this tutorial for more details.
Hey patthehat033, I know that MR DNA has updated their fastq processor recently. It looks like they have made it simpler to upload raw illumina data into Qiime2. I tried it just last week, and there were three files generated: forward.fastq, reverse.fastq, and barcodes fastq. I followed the Atacama soil" tutorial, and things look to be going smoothly. Hope this helps. I have really been enjoying Qiime2, I just recently made the change!!
