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MicroB3-IS / osd-analysis

Repository for all Ocean Sampling Day related source code with information on how-to acquire OSD data
Apache License 2.0
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normalized 16S/18S? #29

Open noaagoodwink opened 8 years ago

noaagoodwink commented 8 years ago

Is the sequencing depth for the taxonomy dataset similar across sites? Has anyone normalized the 16S/18S data? thanks - Kelly

pbuttigieg commented 8 years ago

Hi @noaagoodwink! The sequencing depth does indeed vary. @genomewalker has produced some plots illustrating this, I believe.

In the 16S18S directory, you can find R scripts which will download and standardise the tag data using either the total sum standardisation (TSS), the cummulative sum standardisation (CSS), or the Hellinger transformation. Each has a different effect on the data, but all should mitigate the effect of sequencing depth heterogeneity.

If there's a different method you'd like us to implement, please let us know.