Everything you ever wanted to know about working with RNA-Seq data but were afraid to ask

  1. Do you work with RNA-Seq data?
  2. Do you plan to work with RNA-Seq data?
  3. Have you ever heard of RNA-Seq data?

If the answer to any of these questions is 'yes' (or even 'maybe') then you should definitely check out this fantastic online guide to all things RNA-Seq:

RNA-seqlopedia

The RNA-seqlopedia provides an overview of RNA-seq and of the choices necessary to carry out a successful RNA-seq experiment

Written by Rodger Voelker and Clay Small of the Cresko Lab at the University of Oregon, it is a fantastically detailed, beautifully written resource to walk you through every step of working with RNA-Seq data.

I wish there were more online guides like this! Here's the Table of Contents, with the 'Analysis' section expanded, to give you a feeling for what it covers:

  1. Experimental Design
  2. RNA Preparation
  3. Library Preparation
  4. Sequencing
  5. Analysis
    • Overview
    • Initial Processing
    • Demultiplexing
    • Removing adapters
    • Trimming
    • Kmer Normalization
    • de Novo Assembly
    • de Bruijn Graph assembly
    • Overlap Layout Assembly
    • Aligning reads to a reference
    • Aligning to a ref. genome
    • Aligning to a transcriptome
    • microRNA Aligners
    • Short Read Aligners Output
    • Annotation of transcripts
    • Differential gene expression
    • Normalization
    • Discrete Discrete Models
    • Continuous Discrete Models
    • Nonparametric Models
    • Choice of Analysis Software
  6. References

101 questions with a bioinformatician #28: Jonathan Eisen

This post is part of a series that interviews some notable bioinformaticians to get their views on various aspects of bioinformatics research. Hopefully these answers will prove useful to others in the field, especially to those who are just starting their bioinformatics careers.

Jonathan Eisen is a man who almost needs no introduction. As a Professor at UC Davis, he holds appointments at the Genome Center and in the Departments of Medical Microbiology & Immunology and Evolution and Ecology. He also holds an adjunct scientist position at the Department of Energy Joint Genome Initiative. If you can't find Jonathan in any one these locations, you should also remember to try his 'other' office.

His research interests focus on the diversity of microbes and the role microbes play in the health of ecosystems. One of his many projects relating to this is the microbiology of the Built Environment network (microBEnet).

You might think that studying at Harvard, winning a Benjamin Franklin Award, being a extremely vocal advocate of open access publishing, and making your name as an evolutionary biologist working for the University of California in NorCal would be enough to uniquely identify anyone on this planet. However, these are all feats that that have been accomplished by Jonathan and his brother Michael.

This leads me to what I consider to be the real highlight of Jonathan's career. Forget about his many accomplishments as a scientist. Also, forget about his key role in popularizing and legitimizing the use of tools such as twitter as an important component of scientific outreach. And definitely forget about his tireless efforts to expose the horrible gender bias present at so many academic meetings. No, the real zenith of Jonathan's career is that he is leading the fight to rid the world of badomics words.

You can find out more about Jonathan by visiting his lab's website, reading his extremely popular Tree of Life blog, or by following him on twitter (@phylogenomics). And now, on to the 101 questions...



001. What's something that you enjoy about current bioinformatics research?

I really like the move to improve visualizations as part of bioinformatics workflows. For example see the work of Holly Bik and her work on the Phinch project.

I also really really like the move for more people to be discussing their work and the work of others on social media.



010. What's something that you don't enjoy about current bioinformatics research?

The challenge of long term funding for open source projects.



011. If you could go back in time and visit yourself as a 18 year old, what single piece of advice would you give yourself to help your future bioinformatics career?

A better understanding of ergonomics.



100. What's your all-time favorite piece of bioinformatics software, and why?

MacClade because it got me into informatics and evolution. The developers (the Maddison brothers) were TAs for a class I took as an undergrad (a course by Stephen Jay Gould)



101. IUPAC describes a set of 18 single-character nucleotide codes that can represent a DNA base: which one best reflects your personality, and why?

- KRB: this is a dash, one of two IUPAC characters that can be used to represent a gap.



DVD bonus materials


KRB: Because of the relative brevity of this interview, I thought that I would also share some answers Jonathan gave me to the questions I also include when asking people to do these interviews (this info sometimes helps me write my introductions):

0111. What is the correct way of describing your current position or title(s)

Guardian of Microbial Diversity.


1000. How long have you been in this role?

My whole life.


1001. In 1–2 sentences, describe what your role entails

I am a secret superhero trying to protect the microbes of the world.

You wait ages to see a tweet about gender bias in science, and then three come along at once!

I uploaded my last post about gender bias in genomics/bioinformatics to my blog late on Sunday night. When I checked my twitter feed on Monday morning I was pleasantly surprised to see how much traffic the post had already generated. I was also amused by the serendipitous nature of seeing the following tweets appear closely together in my timeline:

 
 

So well done to the Crick Institute regarding the news that they will have a perfectly equal mix of male and female group leaders. This figure of 50% females would put them top of my list of research institutes in this field.

In contrast, finding out that the new Barcelona Institute of Science and Technology has an all male roster (11 Professors, 18 staff in total) is kind of depressing. This result would put them bottom of my list.