Skip to content
This repository has been archived by the owner on Mar 17, 2023. It is now read-only.

Latest commit

 

History

History
168 lines (124 loc) · 3.48 KB

learning-goals.md

File metadata and controls

168 lines (124 loc) · 3.48 KB
Raw

Learning goals

The purpose of this document is to hold the learning goals for teaching bioinformatics to beginners

For lesson plans, check :

  • Software Carpentry's lessons
  • Rosalind problems for biology-specific programming problems to practice with Python
  • Python for Biologists
  • Python Data Science Handbook

Table of Contents

Proposed schedule

  1. Week 1. Goal: 2.
    1. Install Anaconda Python - Ahead of time
    2. Start a Jupyter notebook -
    3. Change default fonts

Brainstorming

Getting set up

Installing ...

  • Anaconda Python
  • PyCharm editor
  • git
  • Starting up a Jupyter notebook
  • Changing the default font (because with Courier you can't tell the difference between 1 "one" and l "ell")
    • Hack is nice
  • Environments??

External resources

  • Googling
  • Stackoverflow
  • Biostars

Potential project-driven tasks

Given a list of genes, get their enriched promoter motifs

Could maybe use RBPs instead of TFs since I know them better

  • grep a gtf file for the gene names and only get "gene" lines
  • use bedtools flank to get upstream 1000bp
  • Unsupervised problem:
    • Use HOMER or other motif enricher and use all genes' upstream sequences as background
      • Get to talk about background which is important
      • HOMER motifs are very satifying
    • Count enriched kmers (using Python??)
      • Do a multiple sequence alignment
  • Supervised problem:
    • Use UCSC genome browser to download transcription factor binding sites
    • Use bedtools intersect to overlap with other bed file

How can students have ownership?

  • Get genes from a paper they picked
  • Use a TF they're interested in

Amy - Assembling contigs

  • Get sanger sequencing reads
  • Assemble subsets into contigs using velvet
  • Align contigs to known sequence using bwa
  • Find mismatches/SNPs using ??? vcftools?

How can students have ownership?

  • Use contigs from something they created

Plotting

  • Get metadata from MACA
  • Convert date strings eg "170517" to an actual date
  • Make histograms of how often something was made

Collaboration (git)

Teach them a bunch of different things and separate the problem into three steps, where steps 1 and 2 are independent and feed into 3.

Command line tools

Unix basics

Modify Software Carpentry lessons

  • ls
    • Anatomy of a command
    • Ls -l
    • Ls -lh
  • chmod
    • Octal codes
    • Chmod 775
    • Chmod ug+r
    • Chmod og-w
  • cd
  • pwd
  • mkdir
    • mkdir folder/subfolder
  • head
    • head -n 17
  • less
    • less -S
  • Tail
    • Tail -n 2
  • Echo
  • Touch
  • Cat
  • Wc
    • Wc -l
  • Cp
  • Mv
  • Rm

Makefiles

Grep

  • Search for specific term
  • Search for lines that don’t match
  • Add lines after
    • E.g. fastq

Awk

  • Select columns
  • Get number of fields

Git

  • Cheatsheets repo

bedtools

  • intersect
  • flank