Hello researchers,
Sorry for my stupid question. I am learning the QIIME2 workflow for analyzing some 16s amplicon NGS fastq data. I found a very nice paper with data and code public available (Article Microbiome convergence enables siderophore-secreting-rhizoba...
) so I decided to reproduce their qiime2 results.In their steps, they cut off the barcode and primer sequences from the raw fastq sequences (Yes, there are really barcode & primer sequences at the front of sequences). However, I did not find any primer sequences in my own NGS fastq files. Does this mean that the sequencing company have removed barcodes, adapters and primer sequences for me?
Also, should I perform quality-control before importing my fastq raw data to QIIME2?
The sequencing company may have removed the primer sequences. Run them through FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Sometimes FastQC failed to check the barcode and primer sequences. In this paper(Article Microbiome convergence enables siderophore-secreting-rhizoba...
), I found barcode and primers sequences in the 5' of the sequences by manually checking. But the FastQC told me there's no adapter sequences. You can download the 16s amplicon raw data in NCBI database under BioProject PRJNA788265.@Péter Gyarmati- Badges
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