2.3 Data filtering
All raw Illumina reads were filtered by removing reads that included
adapter sequences, duplicated sequences, unknown nucleotides greater
than 10%, and low-quality bases (quality scores ≤ 5) greater than 50%.
Hi-C reads that contain adapter sequences or less than 50 bp in length
were removed, and only PE Hi-C reads were retained. Bases with a quality
score of less than 20 at both ends of the reads were eliminated. All
RNA-seq reads were filtered by removing reads with sequencing adaptors,
unknown nucleotides (N ratio > 10%), and low quality
(quality scores ≤ 5).