Elementolab/Compare Intervals
From Icbwiki
(Difference between revisions)
| Revision as of 03:06, 29 October 2009 Ole2001 (Talk | contribs) ← Previous diff |
Revision as of 03:07, 29 October 2009 Ole2001 (Talk | contribs) Next diff → |
||
| Line 12: | Line 12: | ||
| -showprofile=INT shows 1 if a peak in intervals1.txt overlaps with at least one peak in intervals2, 0 otherwise | -showprofile=INT shows 1 if a peak in intervals1.txt overlaps with at least one peak in intervals2, 0 otherwise | ||
| - | -show_v_int=INT shows which intervals of intervals2.txt overlap with the intervals of intervals1.txt | + | -show_v_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. | ||
Revision as of 03:07, 29 October 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:
-showprofile=INT shows 1 if a peak in intervals1.txt overlaps with at least one peak in intervals2, 0 otherwise -show_v_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.
