This pipeline is a complete analysis of whole transcriptome RNA-Seq data from unaligned reads to a list of differentially expressed genes. The alignment is based on the two-step alignment method for Ion Proton™ transcriptome data. It includes trimming of adapters and bases, followed by initial alignment with Tophat2. The unaligned reads are then re-aligned with Bowtie2. The resulting aligned reads from both the Tophat2 and the Bowtie2 steps are combined into one data node, quantified against a known transcriptome and analyzed for differential gene expression using Partek Gene Specific Analysis.
Requirements: Unaligned reads from a whole-transcriptome RNAseq. Samples MUST have attributes for comparison in the Gene Specific Analysis. Pipeline compatible with Partek Flow 3.0 or later.