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2.8 years ago
sujasubramanian
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70
I am trying to build a computational model to predict TF binding site based on Chip seq data (.narrowPeak), the data contains an intensity value corresponding to each binding region. Can i use this value as a feature to predict the region, any suggestions.
Can you clarify your problem a bit more? Are you inquiring about what the intensity value represents? Is the narrowPeak file the only input you're going to use? Why won't any of the established TF binding site methods do?
i am taking start, end and chromosome no from .narrow file. And i use Microarray gene expression values also for my study. Gene expression and TFs (binding site) details, if i am using intensity of TF binding region as one of the feature how can i treat those intensity measures? column 7 indicates intensity 2.74497 4.36821 10.33905
chr21 9825324 9827741 . 1000 . 2.74497 164.24833 159.38104 1798 chr20 26188685 26190663 . 1000 . 4.36821 127.28879 122.72253 1420 chr1 12508603 12509563 . 1000 . 10.33905 106.66706 102.27689 470 chr6 68598519 68599658 . 1000 . 16.07275 103.14953 98.8843 657