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2017 Short-Read Sequencing Analysis Workshop

Short-Read Sequencing Analysis Workshop
When Jul 10, 2017 09:00 AM to
Jul 21, 2017 03:00 PM
Where JSCBB A108
Contact Name
Contact Phone 303-735-1255
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We are happy to announce we will be holding another Short-Read Sequencing Analysis workshop this summer, July 10-21. The goal of this workshop is to teach the fundamental computational skills necessary for many short read sequencing analyses. In the first five days of this course participants will learn basic Unix/Linux, how to use large compute servers, sequencing read quality control, and read mapping. In the second week we will cover the basic fundamentals of commonly used genomic short read sequencing approaches including basic pipelines for genome re-sequencing, ChIP-Seq and differential expression for RNA-Seq. Our goal is to provide the basic skills necessary for participants to be enabled to learn how to analyze their own data after the course (though some self-study after the course will be necessary).

The format of this course will be a reverse classroom. Attendees will be asked to watch video lectures outside of class. During classroom time (9am to noon daily) attendees will be working through example analysis. In addition, each day we will provide attendees with homework activities that they will need to complete before the next day's classroom time. Help sessions will be available each afternoon.

Schedule

Classroom sections will be held daily from 9am-noon in JSCBB room A108. Office hours/homework sessions will be held daily from 1pm-3pm in JSCBB room A104
Day 1 (July 10) Introduction to short-read sequencing, experimental design & library QC
Day 2 (July 11) Introduction to Linux
Day 3 (July 12) Cluster Usage and Data Transfer
Day 4 (July 13) Sequencing Data QC
Day 5 (July 14) Skills Assessment Day
Day 6 (July 17) Introduction to Read Mapping and Visualization
Day 7 (July 18) DNA Resequencing and Variant Calling
Day 8 (July 19) ChIP-Seq Data Analysis (Peak Calling)
Day 9 (July 20) RNA-Seq Data Analysis and Differential Expression
Day 10 (July 21) Overlapping Data Sets

Registration

This workshop is open to both CU researchers as well as to the local bioscience industry for free due to generous funding from the State of Colorado Office of Economic Development and International Trade. Please register at our EventBrite page.

Registration does NOT guarantee admittance. Spots are limited, so please commit to attending the entire 2-week workshop. This is an intense 2 weeks, please do not plan to work in the lab during this time, the videos and homework assignments will take up significant time outside of the classroom sessions. 

Other information

Please be aware that we will not cover many aspects of sequence analysis due to time constraints. This workshop is designed as an introduction to the most common applications of short-read sequencing and will NOT cover more specialized applications such as metagenomics, specialized RNA-seq or DNA-seq applications (eg. ATAC-Seq, GRO-Seq, etc), or de novo assembly of either genomes or transcriptomes. If you are interested in future workshops covering these applications please email biof-ngs@colorado.edu. 

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