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. 2024 Dec 4;6(4):lqae156. doi: 10.1093/nargab/lqae156

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© The Author(s) 2024. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.

This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.

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Figure 3. — Baited fragment classes and bait analysis. We have expanded our illustrations of re-ligations between restriction fragment ends and resulting chimeric fragments (Figure 1B) and arranged them according to the two observed configuration patterns (Figure 2D). The baits are drawn at the outermost ends of the restriction fragments ( and ). For each configuration, the corresponding chimeric fragments are shown along with the associated bait. (A) For BFC1, chimeric fragments associated with the 5′ end of the baited fragment predominate. (B) In contrast, for BFC2, chimeric fragments associated with the 3′ end of the baited fragment predominate. (C) Distributions of the distances between baits and the 5′ and 3′ ends of bilaterally baited BFC0, BFC1 and BFC2 fragments with shifted baits for the MAC-M0 CHi-C dataset. (D) Distributions of GC content (‘Materials and methods’ section) of baits at the 5′ and 3′ ends of BFC0, BFC1 and BFC2 fragments with unshifted baits for the CHi-C dataset for the same dataset.

Inline graphic — Baited fragment classes and bait analysis. We have expanded our illustrations of re-ligations between restriction fragment ends and resulting chimeric fragments (Figure 1B) and arranged them according to the two observed configuration patterns (Figure 2D). The baits are drawn at the outermost ends of the restriction fragments ( and ). For each configuration, the corresponding chimeric fragments are shown along with the associated bait. (A) For BFC1, chimeric fragments associated with the 5′ end of the baited fragment predominate. (B) In contrast, for BFC2, chimeric fragments associated with the 3′ end of the baited fragment predominate. (C) Distributions of the distances between baits and the 5′ and 3′ ends of bilaterally baited BFC0, BFC1 and BFC2 fragments with shifted baits for the MAC-M0 CHi-C dataset. (D) Distributions of GC content (‘Materials and methods’ section) of baits at the 5′ and 3′ ends of BFC0, BFC1 and BFC2 fragments with unshifted baits for the CHi-C dataset for the same dataset.