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  • Same sample sequenced three times - statistics help

    Hi there,

    I had a purified PCR product (16S mixed bacterial community) and produced three different libraries from the same PCR product. These three libraries were then run through the Illumina MiSeq to have a look at the repeatability of library prep and down stream analysis.

    After processing, the communities of the three libraries look very similar visually in a stacked bar and relative abundances look comparable (e.g. The relative abundance of Firmicutes is 44.99, 45.34 and 46.46% across the three samples) but does anyone know if there is anyway of analysing this statistically? The sample is from the rumen of cattle and contains many different genera.

    I appreciate any help anyone can offer. This is my first post here so I apologise if I've missed any details.

  • #2
    do you only have the 3 samples? I'd look at a dissimilarity measure (bray-curtis is a good one) and see how similar they are. if you have triplicates of many samples then plot the dissimilarities in an NMS (visual check) or run something like Permanova to get a p-value
    Microbial ecologist, running a sequencing core. I have lots of strong opinions on how to survey communities, pretty sure some are even correct.

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    • #3
      Thanks for your quick reply. Yes - just the three samples for this particular analysis. I've attached an example of the data to this message.

      Will give Bray-Curtis a go, thanks again.
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