Elementolab/ChIPseeqer Tutorial
From Icbwiki
(Difference between revisions)
| Revision as of 20:14, 10 November 2010 Eug2002 (Talk | contribs) ← Previous diff |
Revision as of 17:26, 11 November 2010 Eug2002 (Talk | contribs) Next diff → |
||
| Line 39: | Line 39: | ||
| * <span style="color:#347C17"> '''Extended Analysis''' </span>: '''Extract (maximum/average) reads count''' for peak regions using [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqerGetReadCountInPeakRegions ChIPseeqerGetReadCountInPeakRegions] | * <span style="color:#347C17"> '''Extended Analysis''' </span>: '''Extract (maximum/average) reads count''' for peak regions using [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqerGetReadCountInPeakRegions ChIPseeqerGetReadCountInPeakRegions] | ||
| - | * <span style="color:#347C17"> '''Extended Analysis''' </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?) |
| ** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/Compare_Intervals Use CompareIntervals] | ** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/Compare_Intervals Use CompareIntervals] | ||
| - | * <span style="color:#347C17"> '''Extended Analysis''' </span>: '''Compare''' two lists of '''RefSeq genes''' (e.g., Which genes are common in the two lists?) | + | * <span style="color:#347C17"> '''Extended Analysis''' </span> - <span style="color:#8B008B"> '''Compare datasets''' </span>: '''Compare''' two lists of '''RefSeq genes''' (e.g., Which genes are common in the two lists?) |
| ** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/Compare_Genes Use CompareGenes] | ** [http://icb.med.cornell.edu/wiki/index.php/Elementolab/Compare_Genes Use CompareGenes] | ||
| - | * <span style="color:#347C17"> '''Extended Analysis''' </span>: Make a '''similarity coefficient matrix''' (based on [http://en.wikipedia.org/wiki/Jaccard_index Jaccard index]) to see which TFs are similar in terms of peaks overlapping, using [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqerComputeJaccardIndex ChIPseeqerComputeJaccardIndex] | + | * <span style="color:#347C17"> '''Extended Analysis''' </span> - <span style="color:#8B008B"> '''Compare datasets''' </span>: Make a '''similarity coefficient matrix''' (based on [http://en.wikipedia.org/wiki/Jaccard_index Jaccard index]) to see which TFs are similar in terms of peaks overlapping, using [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqerComputeJaccardIndex ChIPseeqerComputeJaccardIndex] |
| Other <span style="color:#AF7817"> '''supplementary tools''' </span> can be found [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_Supplementary here] | Other <span style="color:#AF7817"> '''supplementary tools''' </span> can be found [http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_Supplementary here] | ||
Revision as of 17:26, 11 November 2010
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 : 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
- 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 using ChIPseeqeriPAGE and iPAGE
- Extended Analysis : Evaluate conservation of peaks using ChIPseeqerCons
- Extended Analysis : Cluster and visualize the detected peak regions (Using the Cluster and Java TreeView programs)
- Extended Analysis : Plot average read density profile in peak regions using ChIPseeqerGetReadDensityProfiles
- Extended Analysis : Plot average read density profile in gene parts: promoters, first exon, first intron, all other exons, all other introns, etc. using ChIPseeqerPlotAverageReadDensityInGenes
- Extended Analysis : Extract (maximum/average) reads count for peak regions using ChIPseeqerGetReadCountInPeakRegions
- 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
Other supplementary tools can be found here
