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FastQC results for 16s reads

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  • 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

  • #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.

    https://igatechnology.com
    Last edited by mastal; 05-22-2018, 03:04 PM.

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    • #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.

      https://monsterbashseq.wordpress.com...ality-control/

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