Hi everyone, thanks for taking the time to read this.
I have some 454 pyrosequencing data from years ago, that was processed by Research and Testing. I would really like to take a look at it on QIIME 2 using an EC2 instance, but I am having a hard time. I converted the .fna and .qual files into a .fastq on QIIME(1) using convert_fastaqual_fastq.py, with the hope of using that to see what I could see. Before attempting to run anything though, I want to make sure that my methodology makes sense, and I’m hoping that someone more familiar with with these file types could tell me what I’m looking at, here.
When I look at the raw data I see lines like this: A-03-[Primer 1]::M02233:62:000000000-A9GLW:1:1116:21355:24484 in the sequence identifier / description fields. This sample identifier might show up in a few entries but with different numbers at the end. It looks like 8 base pair barcodes are present at the beginning of the sequences (5’ end) and in quality data, and the primers were removed? Is there an easy way to see whether this is single end or paired end? I’m trying to figure out whether it’s demultiplexed, and whether I can import this kind of data into QIIME 2 and have any hope of getting meaningful interpretations out of it. This isn’t EMP or Casava 1.8 data from what I can see, but is the generated fastq file (from fna + qual) best fit to multiplexed fastq data, or by using a manifest file?
Any thoughts or advice on this would be very welcome. I really appreciate your time.