Hello, I really new in bioinformatics and qiime2 and did all the examples you guys made and thought that i would be pretty easy to get things to work when I recieved my data. Well, it seems it´s the other way around.
First, the paired-end raw data I reciebed has the filename “Sam1-16_S29_L002_R1_001.fastq.gz” and “Sam1-16_S29_L002_R1_001.fastq.gz” but i dont seem to have an barcode.fasta.qz archive. So I cant do the EMP protocol multiplexed paired-end fastq.
On another hand, I have a xxx-full.fasta and xxx-full.qual and the sequencing company described them as: “These files are simply merged and reoriented in the 5’-3’ direction and <200bp sequences removed. This is still (apart from joining the R1 and R2) raw data with the barcodes in them… you can use thes files directly (similar to 454 or PGM data) along with the mapping2 file in secondary analysis software such as qiime or mothur.”
I think I´ll have an easier start point using these 2 files but I can´t find how to import these 2 files into QIIME2.
QIIME2 supports importing raw data in several different formats. It sounds like your data are per-sample CASAVA1.8 format. They do not have associated barcode files, but that’s okay — each sample has already been demultiplexed into its own file.
Alternatively, you might have barcodes in the reads (this is not clear from your description). If that’s the case, please see this community tutorial.