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In this analysis you can find the peaks that are, at a given distance, away from the genes promoters.

In particular, the script:

  • defines the promoters regions (choose an appropriate upstream/downstream length)
  • finds the peaks that do not overlap with the promoters
  • for those non-overlapping peaks, finds those that are at least a given distance away from the promoters.

1.Go to the ChIPseeqer-1.0 directory

$ cd ChIPseeqer-1.0/

2. Type the command:

$ ./FindDistantPeaks --targets=TF_targets.txt --lenu=2000 -lend=2000 --prefix=DIST_PEAKS --db=RefGene -distance=10000

The following options are available:

--targets=FILE file containing genomic regions
--lenu=INT     length upstream of TSS
--lend=INT     length downstream of TSS
--suffix=STR   suffix for output files
--db=STR       can be either RefGene or AceView. Default is RefGene
--distance=INT minimum distance from the promoters

IMPORTANT: Note that in the --targets option you must enter the ChIPseeqer output file.

3. See the results. The output of this process are three files with the extensions: .NOV_PEAKS and .DIST_PEAKS

  • The file that ends with .NOV_PEAKS contains the peaks that don't overlap with the promoters.
  • The file that ends with .DIST_PEAKS contains the peaks that were found to be distant from the promoters for the given distance. This file will look like this:
chrY	2867287	2867611	119
chrY	2871627	2871971	120
chrY	2944779	2944956	120
chrY	5642923	5643407	123
chrY	6905840	6906263	120
chrY	6917898	6918357	120
chrY	6945356	6945877	123
chrY	7267607	7267819	122
chrY	7381389	7381767	123
chrY	7652223	7652533	122
chrY	7659894	7660062	122
chrY	8463843	8464207	123

Each row represents a peak, whereas the columns indicate:

Chromosome	Peak_Start_Position	Peak_End_Position	Number_of_promoters_distant_from_the_peak
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