swo
commented
8 years ago I have a philosophical thing here: I only thought rarefying was good when you were comparing, say, species richness between samples.
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003531
what are other situations when it's demonstrably important?
On Thu, May 19, 2016 at 10:49 PM Joseph Elsherbini notifications@github.com wrote:
often when comparing samples it's important to normalize the number of reads/sample somehow. The simplest and saddest way to do this is to define some threshhold, throw out all samples with fewer reads than that threshold, and sub-sample the other samples to have the same number of reads.
Is this a feature worth adding to caravan? Looks like QIIME has a python implementation: http://qiime.org/scripts/single_rarefaction.html (their github repo here: https://github.com/biocore/qiime/tree/master/scripts)
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elsherbini
often when comparing samples it's important to normalize the number of reads/sample somehow. The simplest and saddest way to do this is to define some threshhold, throw out all samples with fewer reads than that threshold, and sub-sample the other samples to have the same number of reads.
Is this a feature worth adding to caravan? Looks like QIIME has a python implementation: http://qiime.org/scripts/single_rarefaction.html (their github repo here: https://github.com/biocore/qiime/tree/master/scripts)