Short Read Workshop Day 1 - Experimental Design Video 1- Why to short read sequence (or not)

Fastq mapping SamBam conversion IGV UCSC visualization Re-seq RNA-seq ChIP-seq Peaks Differential Expression Variant Calling Quality ✔ Seq !!!!

Informatics is the Bottleneck We can generate sequence data much faster/more easily than we can analyze it Some data is more standard and not has hard to analyze Some needs custom analysis

Short Read Bioinformatics: What you can learn in a week… Decisions which need to be made before you sequence Linux, command line, and clusters How to map reads to a genome Which programs to use for common data analysis pipelines How to look up more information NOT: All of bioinformatics in 8 days

Syllabus Day 1: Exp. Design Instructors: Mary Allen/Tim Read Day 2: Intro Linux & Editors Instructors: David Knox/Joey Azofeifa Day 3: QC, barcodes, intro mapping Instructors: David Brazel /Amber Sorenson Day 4: Moving, clusters, notes Instructors: Joey Azofeifa /Daniel Malmer Day 5: Mapping and viz Instructors: Jess Vera /Phil Richmond Day 6: Reseq Instructors: Phil Richmond /Aaron Odell Day 7: Txpn (RNA-seq) Instructors: Aaron Odell/Mary Allen Day 8: Peak calling (ChIP) Instructors: Li Wang /Amber Sorenson Week 1Week 2

Course structure Before class: – Videos ( – Firefox does not always work. Use Chrome, Internet Explorer or Safari During class (9 am-12 pm) – Examples with example files (fastq, sam, bam, bed) After class (12-5 pm) – Homework

What is short read seq

Next Generation Sequencing “ChIP-Seq Experimental design and analysis strategies” Sven Heinz, UCSD

HOW TO ASK A SEQUENCING QUESTION

The scientific method

Example Questions In Down Syndrome there is a extra copy of chromosome 21, is there extra expression of every gene on chromosome 21? Which genes are up-regulated by my transcription factor?

The scientific method

Literature search Has someone already answered this question? Is there data already available to answer this question?

Example hypothesis A mutation in gene A increases the number of de novo mutations in an organism Adding drug B to the cells increases transcription of most splicing factors RNAi of gene C alters the binding sites/motif of Transcription Factor D

The scientific method

6 people who sequence “A Field Guide to Genomics Research” Plos 2014

Your great idea Seq !!!!