2.6 RNA-seq read pre-processing
For a detailed workflow of the bioinformatic and statistical analyses,
see Supplementary Figure S2. Raw reads were inspected with FastQC
(v0.11.9) (Andrews, 2010) and MultiQC (v1.9) (Ewels et al., 2016)
and trimmed with Fastp (v0.21.1) (Chen et al., 2018) using a
sliding window of 4 bp, a mean Phred score of 30 and reads <
30 bp were trimmed. Kraken2 (v2.0.9) (Wood et al., 2019) was used
with a confidence of 0.3 to remove any contamination using the NCBI
bacterial and archaeal reference libraries (downloaded 08/2020).