Illumina HiSeq 2000 paired end sequencing
Stranded RNA-seq dataset to assess genome-wide gene allelic expression in multiple tissues from the same individual
RNA-seq libraries were generated using the TruSeq stranded RNA sample preparation kit (Illumina) following standard protocols. Libraries were sequenced to a read length of 100bp. Reads were trimmed using Trim Galore v.0.3.3 and aligned to the swine reference genome (Sscrofa10.2) using Tophat v.2.2.10 using the -M option, the -G option, setting the -g option to 1, the –read-realign-edit-dist to 0, --mate-inner-dist to 120, --mate std-dev to 260, and using the fr-firststrand option. Resulting alignments were re-aligned with GATK v2.3-9 and PCR duplicates removed using Picard v.1.119