2.4.2 RNA-seq reads, pre-processing and alignment
The raw paired-end reads were trimmed and quality controlled by Fastp
with default parameters (Chen et al., 2018). And then, clean data from
the samples were used to perform de novo assembly with Trinity (Grabherr
et al., 2011). To increase the assembly quality, all the assembled
sequences were filtered by CD-Hit. To obtain the number of reads
compared to the assembled transcripts which were used for subsequent
expression analysis, the clean reads of each sample were compared with
the reference sequence obtained from the Trinity assembly using Bowtie2.