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).