title: zebra finch habituation: E_Mid
design: Adaptor sequences and low-quality bases were trimmed from the raw sequencing data using Trim Galore (Martin, 2011) and quality control analysis was conducted using FastQC. Trimmed reads were aligned to the NCBI zebra finch reference genome GCF_003957565.2 assembled by the Vertebrate Genomes Project, using STAR v2.7.10a (Dobin et al., 2013) with the quantMode option to provide output in transcriptome coordinates. Gene-wise expected read counts were computed using RSEM (Li & Dewey, 2011)