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Sequencing adaptors, low quality reads, and bases were trimmed using the Trimmomatic-0.38 tool12. The sequence reads were aligned to the human reference genome (hg19) using STAR 2.713. For the whole transcriptome alignment with the STAR, files of the gene model annotations and known transcripts were downloaded from the Illumina’s iGenomes website (http://support.illumina.com/sequencing/sequencing_software/igenome.html).
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