Elementolab/ChIPseeqerThres use

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Using this perl script you can run ChIPseeqer and ChIPseeqerSummary for different values of threshold (e.g., t=5, 10, 15, 20, 25)

1.Go to the ChIPseeqer-1.0 directory.

$ cd ChIPseeqer-1.0/

2. Type the command:

$ perl ChIPseeqerThres --chipdir=CHIP --inputdir=INPUT --pref=CTCF --format=bed

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.
--format=STR      format of the read files: mit, bed, or eland. Default is eland.
--pref=STR        prefix for the output data
--db=STR          can be either RefGene or AceView. Default is RefGene.

3. See the results.

The output of this analysis will appear on the screen:

For t=5 : 
 Peaks    29020 CTCF_TF_targets_5.txt
 Genes     5243 CTCF_TF_targets_5.txt.SUM
For t=10 : 
 Peaks    20532 CTCF_TF_targets_10.txt
 Genes     3241 CTCF_TF_targets_10.txt.SUM
For t=15 : 
 Peaks    16990 CTCF_TF_targets_15.txt
 Genes     2573 CTCF_TF_targets_15.txt.SUM
For t=20 : 
 Peaks    14593 CTCF_TF_targets_20.txt
 Genes     2174 CTCF_TF_targets_20.txt.SUM
For t=25 : 
 Peaks    12844 CTCF_TF_targets_25.txt
 Genes     1922 CTCF_TF_targets_25.txt.SUM

while the output files can be found in the ChIPseeqer directory.

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