Elementolab/Compare Intervals
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| -minoverlap=INT defines the minimum overlap between two peaks. Default is 0 (overlap>minoverlap) | -minoverlap=INT defines the minimum overlap between two peaks. Default is 0 (overlap>minoverlap) | ||
| - | -show_ov_int=INT shows which intervals of intervals2.txt overlap with the intervals of intervals1.txt | + | -show_ov_int=INT shows which intervals of intervals2.txt overlap with the intervals of intervals1.txt |
| The output would still be the intervals in the first file that overlap with at least one interval in the second file. | The output would still be the intervals in the first file that overlap with at least one interval in the second file. | ||
| '''IMPORTANT''': To go a step further and retrieve the corresponding genes (whose promoters overlapped with the output of this analysis, use [[http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_Summary ChIPseeqer Summary]]) | '''IMPORTANT''': To go a step further and retrieve the corresponding genes (whose promoters overlapped with the output of this analysis, use [[http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_Summary ChIPseeqer Summary]]) | ||
Revision as of 18:10, 5 November 2009
COMPARE INTERVALS
This analysis includes comparing two ChIPseeqer outputs (i.e., two lists of detected ChIPseq peaks) and finding the peaks that overlap, at least in one position.
- To run the script, type the command:
$ ./CompareIntervals -intervals1 intervals1.txt -intervals2 intervals2.txt
(intervals1.txt and intervals2.txt should be in ChIPseeqer output-type format in order to find overlapping peaks between ChIPseq runs).
The following options are available:
-minoverlap=INT defines the minimum overlap between two peaks. Default is 0 (overlap>minoverlap) -show_ov_int=INT shows which intervals of intervals2.txt overlap with the intervals of intervals1.txt
The output would still be the intervals in the first file that overlap with at least one interval in the second file.
IMPORTANT: To go a step further and retrieve the corresponding genes (whose promoters overlapped with the output of this analysis, use [ChIPseeqer Summary])
