Elementolab/ChIPseeqer Tutorial
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| * <span style="color:#347C17"> '''Extended Analysis''' </span>: '''Cluster''' and '''visualize''' the detected peak regions using [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_Cluster ChIPseeqerCluster] | * <span style="color:#347C17"> '''Extended Analysis''' </span>: '''Cluster''' and '''visualize''' the detected peak regions using [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_Cluster ChIPseeqerCluster] | ||
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| - | * <span style="color:#347C17"> '''Extended Analysis''' </span>: '''Plot average read density profile in gene parts''': promoters, first exon, first intron, all other exons, all other introns, etc. using [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqerPlotAverageReadDensityInGenes ChIPseeqerPlotAverageReadDensityInGenes] | ||
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| - | * <span style="color:#347C17"> '''Extended Analysis''' </span>: '''Plot average peak numbers in gene parts''': promoters, first exon, first intron, all other exons, all other introns, etc. using [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqerPlotAveragePeaksNumberInGenes ChIPseeqerPlotAveragePeaksNumberInGenes] | ||
| * <span style="color:#347C17"> '''Extended Analysis''' </span> - <span style="color:#8B008B"> '''Compare datasets''' </span>: '''Compare''' two lists of '''peaks'''; (e.g., Which peaks overlap ? Are there any peaks in the first list with no overlap in the second one?) | * <span style="color:#347C17"> '''Extended Analysis''' </span> - <span style="color:#8B008B"> '''Compare datasets''' </span>: '''Compare''' two lists of '''peaks'''; (e.g., Which peaks overlap ? Are there any peaks in the first list with no overlap in the second one?) | ||
Revision as of 20:38, 4 February 2011
Elementolab/ChIPseeqer_Install
ChIPseeqer TUTORIAL
This is a comprehensive step-by-step tutorial on how to use the ChIPseeqer tools to analyze ChIP-seq data.
To run the tools directly from any folder, you need to add the $CHIPSEEQERDIR and $CHIPSEEQERDIR/SCRIPTS to your $PATH variable. Read How to set the CHIPSEEQERDIR variable.
- Core Analysis : Quality Control: QC analysis for the raw reads
- Core Analysis : Peak detection: Split raw data then run ChIPseeqer
- Core Analysis : Gene-level annotation of peaks (Exons/introns/promoters/downstream extremities) and genomic distribution using ChIPseeqerAnnotate
- Core Analysis : Quick promoters summary of peaks using ChIPseeqerSummaryPromoters
- Core Analysis : Create data tracks for the UCSC Genome Browser
- Visualize peak locations in UCSC Genome Browser using ChIPseeqerPeaksTrack
- Create a read density track for the UCSC Genome Browser using ChIPseeqerMakeReadDensityTrack
- Core Analysis : Use ChIPseeqerRun if you want to run the 3 first steps of the Core Analysis (QC, Split in reads-Peak detection, Gene annotation) fast with a single command.
- Extended Analysis : Nongenic annotation using ChIPseeqerNongenicAnnotate
- Extended Analysis : Motif discovery
- De novo regulatory element discovery using ChIPseeqerFIRE and FIRE
- Find peak matches to known transcription factor binding sites using ChIPseeqerMotifMatch
- Extended Analysis : Pathways analysis
- Look for enriched pathways using ChIPseeqeriPAGE and iPAGE
- Find pathway matches to peaks/genes using ChIPseeqerPathwayMatch
- Extended Analysis : Evaluate conservation of peaks using ChIPseeqerCons
- Extended Analysis : Estimate average read density profiles in genes or peak regions using ChIPseeqerDensityMatrix
- Extended Analysis : Extract (maximum/average) reads count for peak regions across multiple ChIP-seq datasets using ChIPseeqerReadCountMatrix
- Extended Analysis : Cluster and visualize the detected peak regions using ChIPseeqerCluster
- Extended Analysis - Compare datasets : Compare two lists of peaks; (e.g., Which peaks overlap ? Are there any peaks in the first list with no overlap in the second one?)
- Extended Analysis - Compare datasets : Compare two lists of RefSeq genes (e.g., Which genes are common in the two lists?)
- Extended Analysis - Compare datasets : Make a similarity coefficient matrix (based on Jaccard index) to see which TFs are similar in terms of peaks overlapping, using ChIPseeqerComputeJaccardIndex
- Extended Analysis - Compare datasets : Make one matrix for each genepart (promoters/exons/introns/distal etc) from multiple peak files in order to find e.g., genes promoters where most of the TFs bind.
Other supplementary tools can be found here
