Chromosome assembly
Adapter sequences of Hi-C raw reads were trimmed, and low-quality
paired-end reads were removed for clean data by using fastp v0.12.6 with
default parameters (Chen, et al. 2018).
Then clean reads were aligned to contig sequences using Bowtie2 (2.3.2,
-end-to-end –very-sensitive -L 30)
(Langmead and Salzberg 2012). Valid
interaction paired reads were identified and retained by HiC-Pro v2.8.1
from unique mapped paired-end reads for further analysis
(Burton, et al. 2013). Invalid read pairs,
including dangling-end, self-cycle, re-ligation, and dumped products
were filtered by HiC-Pro v2.8.1 (https://github.com/nservant/HiC-Pro).
And then, the congtis were clustered, ordered, and oriented onto
chromosomes by LACHESIS (https://github.com/shendurelab/LACHESIS), with
parameters CLUSTER_MIN_RE_SITES=100, CLUSTER_MAX_LINK_DENSITY=2.5,
CLUSTER NONINFORMATIVE RATIO = 1.4, ORDER MIN N RES IN TRUNK=60, ORDER
MIN N RES IN SHREDS=60. Finally, placement and orientation errors
exhibiting obvious discrete chromatin interaction patterns were manually
adjusted.