RNA-seq of Japanese quail
V4-V5 region full length reads were obtained using Illumina Miseq 250-bp paired end reads. The resulting PCR products were purified and loaded onto the Illumina MiSeq cartridge according to the manufacturer instructions. Using PhiX control following the manufacturer instructions, the quality of the run was checked internally and with the help of the previously integrated index, each pair-end sequence was assigned to its sample. Each pair-end sequence was assembled using Flash software (Mago and Salzberg, 2011) with at least a 10-bp overlap between the forward and reverse sequences, which allow 10% of mismatch (Lluch et al., 2015). The absence of contamination was checked with a negative control during the PCR (water as template).