Transcriptome Analysis of RNA-Seq Data

Raw pair-end reads (50+25 bp) were obtained from the SOLID4 System (Applied Biosystems) in color space format (*.csfasta) and were filtered for quality. The adaptor sequences were trimmed, and the reads were aligned to the UCSC human reference genome (hg19) using the Applied Biosystems Bioscope software (Applied Biosystems Bioscope, Thermo Fisher Scientific, Waltham, MA, USA) to obtain reads in the BAM format. Mapping to multiple locations was permitted. The aligned read BAM files were assembled into transcripts, their abundance was estimated and tests for differential expression were processed using the Bioconductor DESeq package (Simon Anders, EMBL, Heidelberg, Germany).^{8 (link)} False discovery rate (FDR) correction for multiple testing was performed according to Benjamini et al.^{9 (link), 10 (link), 11}