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  • MiniMicrobe
    Junior Member
    • Nov 2015
    • 6
    #1

    FastQC results for 16s reads

    Hi

    I have some FastQC results I have generated from Illumina 16s sequences. I have attached an example of the results for one of the demultiplexed fastq files, but they all look simillar.

    I think that the per base quality score looks ok but I am not sure about the other statistics. I have only worked with WGS data before and I haven't been able to find any information on if these are normal.

    Any information/links to resources on if these look ok would be really helpful.

    Thanks
    Michelle
    Attached Files
    Tags: 16s, fastqc, metagenomics, quality check
  • mastal
    Senior Member
    • Mar 2009
    • 666
    #2
    I think they look OK. The thing with 16S reads is that they are amplicons, and that all the
    sequences are very similar.

    I had seen a document on the website of an Italian company named IGATech some months ago,
    which showed typical FastQC plots for 16S data, and improved plots with their method,
    which I think involved some type of heterogeneity spacers, but I can't find it now.

    IGATech - Beyond Sequencing - IGATech
    https://igatechnology.com
    IGATech provides state-of-the-art DNA and RNA sequencing on Illumina, Oxford Nanopore, and AVITI Element Biosciences platforms, offering solutions for agrigenomics, human genetics, cancer studies, pharma and biotech applications, epigenomics, and metagenomics.
    Last edited by mastal; 05-22-2018, 03:04 PM.

    Comment

    • MiniMicrobe
      Junior Member
      • Nov 2015
      • 6
      #3
      Hi Mastal

      Thanks for the reply. I thought that might be the case, I'm just trying to understand the data better.

      I managed to find a bit of a tutorial about this too.

      Workshop on Genomics (Notes, Day 3) – Sequence Data Quality Control
      https://monsterbashseq.wordpress.com/2014/01/15/workshop-on-genomics-notes-day-3-sequence-data-quality-control/
      Use this link for starting AWS instance: Today’s lab topic: Quality control is important: sequencing, library prep Given sequence files from instruments, quality scores, Phred – Wiki is…

      Comment

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