New Analysis Section Idea: Patterns and Pitfalls

### What are the goals of this new example analysis?

As we identify common patterns that people encounter in refine.bio, we should think about ways we can address these in examples. Here I am thinking of things that are not a particular analysis, but that would be common to multiple potential analyses. In a way, I am thinking about some of the things that are in the [refine.bio FAQ](http://docs.refine.bio/en/latest/faq.html), but might not be well addressed in that context. Think of it as the online supplemental materials for the FAQ.

I am calling it Patterns and Pitfalls, because I started thinking about it as common pitfalls, but that was too negative, and alliteration always amazes.

Some examples of things I am thinking about (I am sure there are more!):

* Replicates in a data set (this was the original inspiration)
* Identifying technical replicates (may include querying SRA?)
* collapsing for RNAseq (for technical replicates)
* specifying more complex models for DE?

* Identifying and dropping outlier samples
* Look at a PCA plot, perhaps?

* I might move identifier mapping to this section?

* Other common challenges that Deepa might have identified?

This is not a "before live" problem.

Start by reviewing the refine.bio FAQ and the repository’s existing example analyses to identify recurring patterns and pitfalls. The issue mentions replicates, outlier samples, identifier mapping, SRA queries, RNA-seq collapsing, differential-expression models, and PCA plots; done would require an agreed scope and a defined set of supplemental examples.

Written by the indexing model from the issue text.