Scripts for analysis of low-input Capture-C experiments, including options for stringent duplicate removal, have been incorporated in CCseqBasic by Jelena Telenius. The CCseqBasicS pipeline, scripts and documentation are available on https://github.com/Hughes-Genome-Group/CCseqBasicS. For low-input experiments, we recommend running the pipeline with the flag --wobblyEndBinWidth 20.
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oudelaar/LowInputCaptureC
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Capture-C analysis script, including options for stringent duplicate removal in low-input Capture-C experiments
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