2.7 Transcriptome analysis
Library construction and sequencing was performed in Perpignan University (Bio-environment platform, Perpignan, France) using one Illumina NextSeq (Illumina, San Diego, CA, USA) high output flow cell. Reads were sequenced in 75 base pairs; single end reads resulting in 25 – 30 million reads per sample. Quality of the metrics are indicated in the supplementary Table 2S. Read quality analysis and alignments were performed on the local Galaxy platform (http://bioinfo.univ-perp.fr). Raw read quality was assessed with FastQC (Andrews 2010) and MultiQC was used to summarize FASTQC results. Phred scores were higher than 30 for more than 90% of the read’s length for all the sequences. Reads were cleaned and adaptors removed with Cutadapt (version 1.16, Marcel (2011)). Cleaned reads were mapped against the genome of European sea bass (Tine et al. 2014) using STAR (version 2.7.8a, Dobin and Gingeras 2016). FeatureCounts (Liao et al. 2014) was used to count read-mapped per transcript.