Protein_bytes WendyBu

Analyzing RNA-seq data with the "Tuxedo" tools

Introduction/tl;dr: I wrote this post as a reference for a few new graduate students in my department that are getting started with RNA-seq data analysis. It begins with an informal, big-picture overview of RNA-seq data analysis, and the general flow of the post outlines one standard RNA-seq workflow, but I wanted to give general audiences a "heads-up" that the post goes into quite a bit of nitty gritty detail that's specific to our department's computing setup.

preliminaries: what's RNA-seq?

RNA-seq is a high-throughput technology used to measure gene expression in cell populations. For a super bare-bones picture of what gene expression is, please enjoy this ASCII art I made to illustrate the process:

[DNA]            ACGTAGGT{CGTATTT}AGCGT{AGCGCCCGA}TTACA
                                    |

	# This code uses Biopython to retrieve lists of articles from pubmed
	# you need to install Biopython first.

	# If you use Anaconda:
	# conda install biopython

	# If you use pip/venv:
	# pip install biopython

	# Full discussion:

	#!/bin/bash

	# viewing environment variables
	echo "The value of the home variable is: "
	echo $HOME

	# issue a command
	echo "The output of the pwd command is: "
	pwd

	"""Information Retrieval metrics

	Useful Resources:
	http://www.cs.utexas.edu/~mooney/ir-course/slides/Evaluation.ppt
	http://www.nii.ac.jp/TechReports/05-014E.pdf
	http://www.stanford.edu/class/cs276/handouts/EvaluationNew-handout-6-per.pdf
	http://hal.archives-ouvertes.fr/docs/00/72/67/60/PDF/07-busa-fekete.pdf
	Learning to Rank for Information Retrieval (Tie-Yan Liu)
	"""
	import numpy as np