Cis-regulatory Element Annotation System on Helix
CEAS is a tool designed to characterize genome-wide protein-DNA interaction patterns from ChIP-chip and ChIP-Seq of both sharp and broad binding factors. It provides statistics on ChIP enrichment at important genome features such as specific chromosome, promoters, gene bodies, or exons, and infers genes most likely to be regulated by a binding factor. CEAS also enables biologists to visualize the average ChIP enrichment signals over specific genomic features, allowing continuous and broad ChIP enrichment to be perceived which might be too subtle to detect from ChIP peaks alone.
Environmental variable need to be set correctly first:
module load ceas
The example files used below can be copied from /fdb/CEAS
First set environmental variables as above.
copy input files from /fdb/CEAS to /data/user/ceas/run1
$ cd /data/user/ceas/run1
$ ceas --name=H3K36me3_ceas --pf-res=20 --gn-group-names='Top 10%,Bottom 10%' -g hg18.refGene -b H3K36me3_MACS_pv
al1e-5_peaks.bed -w H3K36me3.wig