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MiniMicrobe 05-22-2018 07:11 AM

FastQC results for 16s reads
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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.


mastal 05-22-2018 04:01 PM

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.

MiniMicrobe 05-24-2018 07:27 AM

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.

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