Taiwan University Some Thoughts on RNA-Seq Practices and Virtual Machine Using • Thanks for everyone’s hard work in advance. • RNA-Seq needs standard samples, which is now collected by 于晴(<- she is in charge) • Genome reference (sequence, annotation, … basically everything) can be found on Illumina iGenome (or `/data/iGenome` on 171) 2013.12 Slides by Liang Bo Wang iga11moon11wave / Twitter
Taiwan University Thoughts on RNA-Seq … (cont’d) • It’s tedious in the beginning, but this is part of the practice, please always try yourself first. – Because most of the time, we are trying. – The goal is to make everyone knows how to debug, understands the error message, and googles. So you will not stop doing when your program stops. – Try to log everything since you need to repeat a lot 2013.12 Slides by Liang Bo Wang
Taiwan University Thoughts on Virtual Machine … (cont’d) • I only provide a very clean installation, so you might need some (translation: a lot of) configuration. • One might install their own tools on VM and might plan to re-run the pipeline on 171/173 – Remember how you install them, so I can run the same commands without looking its documentation. For example, $ yum install strange-deps-dev $ wget http://dont.like.valentine/src/mytool_v5.56.6.tar.gz $ tar zxvf mytool_v5.56.6.tar.gz; cd mytool $ make $ sudo make install 2013.12 Slides by Liang Bo Wang