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Counting of regions within a segment DrD2009 Bioinformatics 0 01-08-2012 10:53 AM

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Old 06-30-2015, 05:21 AM   #1
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Post Counting DNA tag sequences in specified regions for ChIP-seq

Now I have 2 chip-seq data.
1) IP of the transcriptional factor for WT cells
2) IP of the transcriptional factor for KO cells

I have found 15000 significant binding sites (bed file) of the transcriptional factor in WT experiment using SICER.
Then, I'd like to count number of DNA tag sequences of KO chip-seq data in each top 5000 binding sites (specified genomic regions) of WT chip-seq data, followed by calculating Z score of tag seqences of KO along WT chip-seq data.

Subsequently, I'd like to make a heatmap using this 2*5000 data matrix of Z-score.
How can I do?
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