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#81 Hi-C alignment
Can Bowtie be modified for Hi-C alignments? For Hi-C experiments, DNA fragments that are far away on a linear DNA strand, but that are brought together by structural proteins, are ligated together and paired-end Illumina sequenced. Hi-C is a little like mated pairs, but the distances between the sequenced ends can be very large (even on a different chromosome), and can be in both orientations.
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