Elementolab/Compare Intervals

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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: 

-overlap_min=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])

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