Elementolab/ChIPseeqer use
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| Each row represents a peak location, whereas the columns indicate: | Each row represents a peak location, whereas the columns indicate: | ||
| - | Chromosome Start_Position End_Position Score Avg_Number_of_Reads | + | Chromosome Start_Position End_Position Avg_p-value Score |
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ChIPseeqer
The second step in this analysis is to run ChIPseeqer.
1.Go to the ChIPseeqer-1.0 directory.
$ cd ChIPseeqer-1.0/
2. Type the command:
$ ./ChIPseeqer.bin -chipdir CHIP/ -inputdir INPUT/ -t 15 -fold 2 -format bed > TF_targets.txt
The following options are available:
-chipdir=DIR directory that contains the ChIP reads (one file per chromosome, named reads.chr1, reads.chr2, etc). -inputdir=DIR directory that contains the input DNA reads. -t=FLOAT significance negative log p-value [ratio] threshold for peaks. Thus, 15 means 10^-15. Default is 15. -fold=FLOAT how much higher ChIP peaks should be compared to input DNA peaks. -fraglen=INT length of the fragments whose extremities have been sequenced. -format=STR format of the read files: mit, bed, or eland. Default is eland. -minlen=INT minimum peak width. Default is 100bp. -mindist=INT mininum distance between peaks (merge subpeaks otherwise). Default is 100bp.
IMPORTANT: The ">" symbol in the command indicates the redirection of the output of the script. Therefore, "> output_filename" indicates the output file. If the redirection is omited the output will be shown on the screen.
3. See the results.
Open the output file (e.g., TF_targets.txt). The results will look like this:
chr9 262661 263289 -122.6845 87.2343 chr9 287536 287808 -19.1936 23.8394 chr9 505597 506148 -47.9809 41.1865 chr9 526545 526776 -16.7959 24.0984 chr9 553490 554074 -31.9228 28.8078 chr9 555467 556045 -32.8033 33.3532 chr9 557296 557800 -38.7768 22.3161 chr9 561241 561516 -18.2769 25.4521 chr9 615745 616124 -23.4549 24.8840 chr9 632232 632383 -18.2943 14.2063 chr9 639304 640100 -52.0510 47.4016 chr9 640412 640733 -22.9267 20.1568
Each row represents a peak location, whereas the columns indicate:
Chromosome Start_Position End_Position Avg_p-value Score
