Resources

FAQ

Biology-centric

I want to learn how to do bioinformatics from the command line - how do I get started?

There web is a great resource to learn any and all things computational. Including some of the links found at the bottom of this page, a good place to start in the Biostars Handbook, authored by Istvan Albert of Penn State University. It contains practical tips for bioinformatics as well as analyzing biological data.

If you have an account, you can access the local instance of Galaxy at tadpole.bx.psu.edu. Otherwise, many of the same tools are also available on the public instance at usegalaxy.org.

I can’t find any help pages or tutorials…how can I get started?

You can learn how to get started using the following links:

I don’t understand whether my data is of high quality or not…how can I check?

See Understanding FastQC Reports (also in the links below). Created by the developers of FastQC, they go on to describe common things that we can see went wrong in the initial QC reports generated using their very versatile tool.

How can I check genome wide coverage distribution?

There are several tools that allow you do qualitatively and quantitatively check this. For viewing purposes, you can view your alignment in IGV. But to quantify this you will want to either:

  • Use a tool that checks various statistics for you
  • Create a custom pipeline to check for you

Tools that are available to do this for you include deepTools and Picard Tools for whole genome and ChIP-seq data sets or RNA-SeQC, RSeQC, or QoRTs for RNA-seq.

Alternatively, if you know which regions of the genome you are interested in, you could also create a custome pipeline with BEDtools and calculate the statistics you care about.

Data-centric

How can I share my data with others?

Essentials

Galaxy Resources

Public Galaxy Servers

Genome Browsers

Useful Blogs

Miscellaneous

Updated - 2016-04-08