Workshop Information

Providing Feedback

While we endeavour to deliver a workshop with quality content and documentation in a venue conducive to an exciting, well run hands-on workshop with a bunch of knowledgeable and likable trainers, we know there are things we could do better.

Whilst we want to know what didn’t quite hit the mark for you, what would be most helpful and least depressing, would be for you to provide ways to improve the workshop. i.e. constructive feedback. After all, if we knew something wasn’t going to work, we wouldn’t have done it or put it into the workshop in the first place! Remember, we’re experts in the field of bioinformatics not experts in the field of biology!

Clearly, we also want to know what we did well! This gives us that “feel good” factor which will see us through those long days and nights in the lead up to such hands-on workshops!

With that in mind, we’ll provide three really high tech mechanism through which you can provide anonymous feedback during the workshop:

1. A sheet of paper, from a flip-chart, sporting a “happy” face and a “not so happy” face. Armed with a stack of colourful post-it notes, your mission is to see how many comments you can stick on the “happy” side!

2. Some empty ruled pages at the back of this handout. Use them for your own personal notes or for write specific comments/feedback about the workshop as it progresses.

3. An online post-workshop evaluation survey. We’ll ask you to complete this before you leave. If you’ve used the blank pages at the back of this handout to make feedback notes, you’ll be able to provide more specific and helpful feedback with the least amount of brain-drain!

Document Structure

We have provided you with an electronic copy of the workshop’s hands-on tutorial documents. We have done this for two reasons: 1) you will have something to take away with you at the end of the workshop, and 2) you can save time (mis)typing commands on the command line by using copy-and-paste.

While you could fly through the hands-on sessions doing copy-and-paste you will learn more if you take the time, saved from not having to type all those commands, to understand what each command is doing!

The commands to enter at a terminal look something like this:

tophat --solexa-quals -g 2 --library-type fr-unstranded -j annotation/Danio_rerio.Zv9.66.spliceSites -o tophat/ZV9_2cells genome/ZV9 data/2cells_1.fastq data/2cells_2.fastq

The following styled code is not to be entered at a terminal, it is simply to show you the syntax of the command. You must use your own judgement to substitute in the correct arguments, options, filenames etc

tophat [options]* <index_base> <reads_1> <reads_2>

The following is an example how of R commands are styled:

R --no-save
library(plotrix)
data <- read.table("run_25/stats.txt", header=TRUE)
weighted.hist(data$short1_cov+data$short2_cov, data$lgth, breaks=0:70)
q()

The following icons are used throughout the documentation to help you navigate around the document more easily:

Question

Questions to answer.

Answer

Answers will be provided at the end of the workskop.

Important

This is important.

STOP

Warning - STOP and read.

Bonus exercise

Bonus exercise for fast learners.

Advanced exercise

Advanced exercise for super-fast learners

Resources Used

We have provided you with an environment which contains all the tools and data you need for the duration of this workshop. However, we also provide details about the tools and data used by each module at the start of the respective module documentation.