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RNA Seq Experiments

I have done a few bulk RNA seq experiments. They seem to be relatively straight forward so far. Here you can find the analysis I did as reference.

  1. Bulk Bacterial RNA sequencing

Creating a metaproteomics database from shotgun metagenomics

To do metaproteomics of the gut microbiome, I have needed to create a matched database from metagenomic sequencing. This is really important to do, because you can use this as a method to constrain the search space that is used to identify peptides from the MS2 peaks. There are many approaches you could take to accomplish this, but here are the ones that I have tried. Once I have figured out how these compare to each other I will post some sort of evaluation.

  1. Qiita

Miscellaneous

Here are a bunch of one off analyses that I don't think are big enough to warrant their own section.

  1. Determining which taxa encode a given protein