Bioinformatics 101 perhaps?

[zianeffy]

Hi,
I just started in a lab that is now interested in doing NGS analysis of samples (RNA-seq, ChIP-seq and DNA-seq). Unfortunately nobody in the lab (or on campus) has done much NGS before so I'm kinda left to myself, and my boss wants me to learn (pretty much from scratch).

I was wondering if you knew of any good, comprehensive resource for beginners, including programming and where to download info from databases and how to handle these big files and such. I don't really have any programming background, but I am a very fast learner. I just need someone to show me the ropes of things. I have a dataset that was produced by someone else but never analyzed, and it's sitting there ready to be handled, but I don't even know where to start. Not sure if it matters, but it was generated on an Illumina machine.

Any help would be greatly appreciated.
Thanks

[GenoMax]

Galaxy is a very nice tool to get your feet wet on the side while you work on getting your server-side software analysis setup going. Plan on picking up *nix skills, if you need to.

Check these links for getting started:

http://main.g2.bx.psu.edu/learn

http://wiki.g2.bx.psu.edu/Learn

Of course the SeqAnswers Wiki is there: http://seqanswers.com/wiki/SEQanswers

[dcfactor]

Getting Started

IMHO this tutorial (http://korflab.ucdavis.edu/Unix_and_Perl/) "A Unix and Perl Primer for Biologists" is a great way to get started learning Unix and Perl, which you will most likely need for NGS analysis in general, unless you plan on trying to stick 100% to the Galaxy user interface.

[pbatzel]

I'm still pretty new to Bioinformatics, but I started out with http://biopython.org/wiki/Main_Page and never looked back. Python is a fairly easy to learn language in my opinion and while biopython isn't the most optimized of libraries, it's pretty good for beginners and has a load of tutorials based on scenarios.

Good luck and let us know if you find anything that's truely comprehensive.

[Bukowski]

Make a cup of coffee (or 10), fire up YouTube:

http://www.youtube.com/user/GenomeTV

[ETHANol]

The 'Unix and Perl Primer for Biologists' mentioned above is great. Does anyone know of anything along the same lines for R/Bioconductor?

Once you get the basics and are ready to look at some RNA-seq data, here is a great workflow/tutorial

http://seqanswers.com/forums/showthread.php?t=7068

If you are looking for some wet lab ChIP-seq protocols you can look at these that I made (be on the look out for typos and little mistakes as I tend live on the lysdexic (dyslexic) side of things):

http://ethanomics.files.wordpress.com/2011/10/chip_covaris.pdf

http://ethanomics.files.wordpress.com/2011/10/chip_truseq.pdf

Good luck. It's easier then it seems at first.

[shandley]

A bit of promotion here, but we have put together a pretty good training opportunity for people starting in Genomics. We focus on the fundamentals and offer Advanced Topic training after the core Workshop. There is an announcement on the SeqAnswers Events forum, or you can check things out on our web site at http://evomics.org.

We are trying to do a Workshop in both the US and in Europe on an annual basis. Of particular note, we are hosting Advanced Topic Sessions on Python/Biopython and R/Bioconductor. We are also working closely with the GMOD and Galaxy communities and will have additional on-site training for both of their systems.

I know it can be tough to get away and find funding for these types of things, but I believe that this is a great way to be immersed in intensive training opportunities and a good opportunity to meet with software developers and quality scientists from around the world. The European Workshop is in the Czech Republic. The location is quite spectacular and a nice place to find oneself even in the middle of Winter.

Cheers,

Scott Handley

[ETHANol]

Any chance the course material will be publicly available for people that do not have the time and/or funding to go to the course?

[shandley]

Yes. We have some of the material from our previous Workshops already on http://evomics.org. We are transitioning to a new site, so we don't have 100% of the old content, but are making progress. Everything should be over and updated by the end of the year.

In addition, we are adding learning activities for topics that we believe are important, but are not necessarily covered during the Workshop. For example, how to use BWA is not an official Workshop topic but we are developing an activity for it. These activities will be geared towards the beginner with a lot of additional content.

Let me know if you have any questions or would like to see something in particular.

Scott

[liux]

I would recommend python for anyone new in Bioinformatics too. if you already knew perl, there is no need to switch. But if you are totally new, python is a cleaner language, easier to learn, but is just as powerful as perl.

I'm still pretty new to Bioinformatics, but I started out with http://biopython.org/wiki/Main_Page and never looked back. Python is a fairly easy to learn language in my opinion and while biopython isn't the most optimized of libraries, it's pretty good for beginners and has a load of tutorials based on scenarios.

Good luck and let us know if you find anything that's truely comprehensive.