FastQC results for 16s reads

MiniMicrobe · 05-22-2018, 07:11 AM

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

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.

https://igatechnology.com

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.

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

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05-22-2018, 04:01 PM	#2
mastal Senior Member Location: uk Join Date: Mar 2009 Posts: 667	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 at 04:04 PM.

05-24-2018, 07:27 AM	#3
MiniMicrobe Junior Member Location: Nottingham Join Date: Nov 2015 Posts: 6	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/