2.7 Quality control and read mapping
The raw paired end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and sickle (https://github.com/najoshi/sickle) with default parameters. The parameters were as follows: 1) trimming the 3’-end low-quality bases (quality value less than 20); 2) removing N-containing reads, 3) discarding adaptor; 4) sequence with length ˂ 30 bp after quality trimming. Finally, the clean reads were mapped to reference genome using Bowtie2 (version 2.2.9) software. The mapped reads of each sample were assembled by StringTie (https://ccb.jhu.edu/software/stringtie/index.shtml?t=example) in a reference-based approach (Pertea et al., 2015).