Can I run CHiCAGO with captureC data?

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Issue #72 new
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I have 4 baits targeting the same locus, but at different adjacent RE fragments. I'm thinking I should just put one line in .baitmap file (as well as the .rmap file), like a big merged region. Is it right?

My second question is about .chinput file. I'm going to convert the output wig file from to .chinput file. The question I have is that, for this wig file, read mapped wihtin +/- 1kb of the bait region are removed. Will it affect the CHiCAGO calculation?

Thanks, Yichao

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