carlalbc / bio634_2020 Goto Github PK

Carla Bello ([email protected]) & Gregor Rot ([email protected])

• 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 – Introductory Course: Assembly, Mapping, and Variant Calling

(Unix System hierarchical tree)

/home/student
            /software
            /variantcalling2
            /rnaseq
            /data
                /data_ngs2

Install Docker. Download the bio634.tar file. Load the Docker image to the file:

docker load -i bio634.tar

Create a storage folder on your local computer. Then you can start the docker container by running:

docker run -v /storage:/home/student/storage --hostname ubuntu --user student --workdir="/home/student" -ti bio634 bash --login

In the case above, the local folder is /storage (replace with your own local folder), which will be mounted on /home/student/storage.

If you are using Windows, please put the local folder in quotes, an example would be:

docker run -v "C:\Users\username\storage":/home/student/storage --hostname ubuntu --user student --workdir="/home/student" -ti bio634 bash --login

We will run most exercises in this Docker container, which has all required software pre-installed.

• 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

• Cheatsheet intermediate
• SIB e-learning: UNIX fundamentals