Case Studies

Here are some case studies to show the powerful capabilities of the ZENBU data processing and visualization system.

Uploading annotation from other sources
We have loaded in zenbu a very large body of annotations from UCSC, Ensembl, ... Yet this is far from being complete. Would you require annotations from third party sources that have not been loaded, here is an example of loading the latest human repeat masker track available from UCSC using their table browser interface ... more

RNAseq exploration
This case study will show case how ZENBU enables multiple views and processing of RNA-seq raw mapped reads (from simply loaded bam files) allowing investigator to not only display the expression as a traditional wig track, but also displaying individual reads, highly redundant reads, contrast experiments thru a heatmap style rendering, extract intron usage and RPKM normalized expression of transcript colocalized with the RNAseq reads... more

ShortRNA denovo clustering
ZENBU enables the dynamic creation of short RNA data clusters, which allows researchers to delineate the structure and expression levels of short RNA from the raw mapping of short RNA fraction sequenced reads. To cluster the reads we employ Paraclu.... more

CHiP-seq novel loci detection
In this case study, we propose to emulate the approach by Mikkelsen et al. in "Genome-wide maps of chromatin state in pluripotent and lineage-committed cells" [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2921165/ Nature. 2007 August 2; 448(7153): 553–560] and use H3K4me3 and H3K36me3 ENCODE ChIP-Seq to uncover genes and non-coding RNA loci... more