The 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 HTSeq and Picard tools to collect assigned 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.