Blog Series: WoG, Cesky Krumlov; Day 3: Genomics Study Design, a.k.a. "To seq or not to seq, that is the question!"

So I totally slacked off today and went to lunch instead of writing the usual afternoon blog of the morning session, I hope you'll all forgive me, but to be fair those of you in the U.S. weren't even out of bed by the time lunch for me rolled around!

All of the presentations so far have been really awesome and informational so I hope you will take advantage of all the slides being posted on the website!

Today's morning session is great for PIs and students wishing to design sequencing experiments and determining to get an NGS platform.

I will be interjecting during this blog post...my interjections will be in a different color (probably green, because I like the color green).

Blog Series: WoG, Cesky Krumlov; Day 2: Data Quality Control--no really it's more fun than it sounds...

In truth...to me, data sequence quality control is necessary and ok and it was fun when I was learning it but the further in you get the more you want to automate the hell out of it! WELL, lucky for you, you probably aren't at that stage yet so we are going to start fresh thanks to Naiara's talk, slides and exercises ala this evenings lab!

It is time, my fellow command-line/terminal apprentice ninjas...let's DO SCIENCE

Now I won't be going through absolutely everything in this blog entry but I will cover most and offer tips to help the exercises go smoothly for you.

Blog Series: Workshop on Genomics, Cesky Krumlov; Preparation--Genome Structure

Section 2: Genomic Structure

The prep section for genomic structure was small with two articles suggested, one of which you'll need a subscription to read; the other is freely available! Huzzah!

• Alkan, C; BP Coe and EE Eichler. 2011. Genome structural variation discovery and genotyping. Nature Reviews Genetics. 12:363-376. (subscription needed)
• Mills, RE et al., 2011. Mapping copy number variation by population-scale genome sequencing. Nature. 470:59-65. (FREE!)

So lets jump into Mills et al. and learn something...the one caveat to this article is they automatically assume you know what a 'structural variant' is and they are specifically talking about this with respect to the human genome. So lets back-track a little--skim if you're already a structural 'pro'...or better yet, add your two cents in the comments along with other links to clarify this topic.