%week%12,%lecture%23% - pennsylvania state …ebola- snp-2014 km034562 03676 03680 03686 03687 03683...
TRANSCRIPT
2014 -‐ BMMB 852D: Applied Bioinforma9cs
Week 12, Lecture 23
István Albert
Biochemistry and Molecular Biology and Bioinforma9cs Consul9ng Center
Penn State
Redoing the SNP calling in the Ebola paper
• Find the supplementary material
• Download the SNP calls they make
Get the supplemental informa9on
Visualize their SNP calls
In class demonstra9on
• See suppor9ng class website for code
• Formalize/understand each step that you need to do
• Collect the requirements and enumerate the steps
Tools that write commands
Some9mes it can be handy to write a tool that generates a series of commands.
You can save and share the script with others and can be rerun with ease.
Even a subset of the data may capture most relevant features
Homework 23
• Call snps from an SRA file that corresponds to one sample of the Ebola genome.
• Compare your calls with those generated by the authors.
• Hint: make sure to use the same reference genome