HOMER
Software for motif discovery and ChIP-Seq analysis
ChIP-Seq Analysis
ChIP-Seq is the best thing that happened to ChIP since the
antibody. It is 100x better than ChIP-Chip since it
escapes most
of the problems of microarray probe hybridization.
Plus it is
cheaper, and genome wide. Chuck would be pleased if he
came up
with the idea.HOMER offers solid tools and methods for interpreting ChIP-Seq experiments. In addition to UCSC visualization support and peak finding [and motif finding of course], HOMER can help assemble data across multiple experiments and look at positional specific relationships between sequencing tags, motifs, and other features. You do not need to use the peak finding methods in this package to use motif finding. (Use the bed2pos.pl program to create peak files from BED files).
NOTE: The current implementation is geared for single tag sequencing.
Background:
Standard ChIP-Seq analysis with HOMER:
- Creating a "Tag Directory" from aligned sequences
- Basic quality control (sequence
bias,
fragment length
estimation)
- Creating files to view your data in the UCSC Genome Browser
- Finding Peaks (ChIP-enriched regions) in the genome
- Finding enriched motifs in ChIP-Seq peaks
- Annotating Peaks (and
cross referencing other experiments and motifs)
Advanced ChIP-Seq Analysis with HOMER:
- Finding overlapping or
differentially bound peaks
- Creating histograms with
sequencing data
- Creating heatmaps with sequencing data
- Re-centering peaks on
motifs
Can't figure something out? Questions, comments, concerns, or other feedback:
cbenner@ucsd.edu