title: Hi-c sequencing of Apocynum venetum leaf: seedling
design: We constructed Hi-C fragment libraries from 300-700 bp insert size as illustrated in DC. Zhang et al, and sequencing through Illumina platform. Briefly, adapter sequences of raw reads were trimmed and low quality PE reads were removed for clean data. The clean Hi-C reads were first truncated at the putative Hi-C junctions and then the resulting trimmed reads were aligned to the assembly results with bwa aligner. Only uniquely alignable pairs reads whose mapping quality more than 20 were remained for further analysis. Invalid read pairs, including Dangling-End and Self-cycle, Re-ligation and Dumped products, were filtered by HiC-Pro (v2.8.1)