The Torrent RNASeqAnalysis Plugin is an RNA Transcript Alignment and Analysis tool for use with reference genomes hg19 and mm10. Use this plugin to analyze cDNA reads, as produced by RNA-Seq. Reads are aligned to the reference genome using STAR and bowtie2 aligners to find full and partial mappings. The alignments are analyzed by Picard tools to collect read counts and cufflinks to extract gene isoform representation. For barcoded data, comparative representation plots across barcodes are created in addition to individual reports for each barcode. All alignment, detail and summary report files are available for download.

For detailed instructions on setting up an RNA Seq Planned Run and reviewing results, see the RNASeq Plugin User Bulletin.pdf