I put a collection of videos on YouTube to help new users getting started using EaSeq (described in this post). I know that it is slightly off, compared to the other tutorials here, to post links to video tutorials. But now that they are made, then I thought that it would be appropriate to mention them here.
The videos cover the following topics:
- How to download and install EaSeq.
- Introduction of the main interface.
- How to import ChIP-seq data and a set of genomic regions into EaSeq (the example data can be downloaded here).
- How to make heatmaps from the imported data above. In the example we visualize histone marks (H3K27me3 and H3K36me3) at CpG-islands and sort them according to their sizes.
- How to access the autogenerated legends and methods.
- How to make superimposed tracks. In the example we visualize histone marks (H3K27me3 and H3K36me3) at CpG-islands.
- How to export plots as tiff files and toggle autoenumeration on/off.
- How to use EaSeq as a genome browser and explore the underlying loci in a heatmap.
- How to download gene annotation data and extract TSSes as new regions.
- How to gate out regions and instruct new plots to show this population.
- How to handle plots and change their settings.
One way to get further is to use the tutorials integrated within the program that guide users through a particular visualization or analysis step by step using own or example data.
- How to run the integrated tutorials and the integrated demo.
All of the steps above are also combined in a 27-minute video.
There is much of EaSeq that is not covered here, and I will have to add new videos / instructions in steps. As I am rather untrained in making video tutorials, then I'd appreciate to get feedback on topics that you would like to see demonstrated or that needs to be explained better.
I am making a page on EaSeq's website that also covers this, and it will be updated as new tutorials are being made.