Carla Bello (carla.bello@ieu.uzh.ch) & Gregor Rot (gregor.rot@uzh.ch)
| 9.30 - 9.40 | Welcome & Introduction | CB & GR |
| 9.40 - 10:45 | QC and Mapping Presentation | Hands-on |
CB |
| 10:45 - 11.00 | Coffee break | |
| 11.00 - 12.00 | QC and Mapping: Continuation | CB & GR |
| 12.00 - 13.30 | Lunch break | |
| 13.30 - 14.30 | Variant Calling 2 Presentation | Hands-on |
GR & CB |
| 14.45 - 15.00 | Coffee break | |
| 15.00 - 16.00 | Talk: Dr. Jean-Claude Walser (ETH): RNA-seq in ecology and evolutionary biology pdf |
| 9.30 - 10.45 | RNA-seq Presentation | Hands-on |
CB |
| 10.45 - 11:00 | Coffee break | |
| 11.00 - 12.00 | Continuation: RNA-seq | CB & GR |
| 12.00 - 13.30 | Lunch break | |
| 13.30 - 14.30 | Continuation: RNA-seq | CB & GR |
| 14.30 - 14.45 | Coffee break | |
| 14:45 - 16:00 | Making sense of gene lists Presentation | Hands-on |
GR & CB |
- Basic command line
- Basic knowledge about NGS data structure: reads, alignments (BAM), quality scores or attendance of "BIO609 Introduction to Linux and Bash Scripting" and "BIO610 Next-Generation Sequencing 1"
Please follow the instruction on https://github.com/grexor/teachingDocker to install and setup the Docker environment we will use during this class.
-
Haddock & Dunn. Practical Computing for Biologists. Sinauer Associates 2011.
A good book that covers the shell/command line, programming in python & bash, databases, regular expressions. Suitable for self-study and as a reference book. -
Vince Buffalo. Bioinformatics Data Skills. O'reilly 2015
This practical book teaches the skills that scientists need for turning large sequencing datasets into reproducible and robust biological findings. Also covers methods on Sequence and Alignment Data. More advanced than Haddock & Dunn and progresses with faster pace.
General
- http://software-carpentry.org/
Scientific Computing Resources for learning bash shell, programming in python, R, …] - SEQanswers the NGS community (Questions&Answers, protocols, software lists, news)
- BioStars for questions about biocomputing and scripting for biologists
- stackoverflow for questions related to coding
Linux/Shell