Elementolab/ChIPseeqer use

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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