Dear Qiime2 team,
Happy new year!
I am trying to learn how to use Qiime2. I have already tried the tutorials and now I am working on my own data.
I am dealing with two runs of pair end data. Unfortunately, I did not get a barcode.fastq file from the sequencing company. I could not find a way to transform my data to what is needed for Qiime2 according to the “Atacama tutorial”, so I have done the following.
- I started off with files provided by the company that had already been joined.
- I then concatenated the fasta files from both runs, as well as the qual files from both runs.
- Converted them to fastq
- Extracted the barcodes with Qiime1 (extract_barcodes.py) without reverse complementing them (when I did reverse them, I only had 3 samples left).
- Compressed fastq files to fastq.gz
- Imported them into qiime2 as single end sequences
- Demultiplex them as single-end reads
- Summarize the data
When viewing the results, I obtain this very weird graph:
I would very much appreciate if anyone could help me understand this graph, and where may I have made a mistake.
Thanks a lot!