RNA-Seq Web Resources

Technical Guides

Discussion Forums

  • The RNA-Seq Blog – A discussion forum for all things transcriptomic.
  • SEQanswers – The next-generation sequencing community – threads tagged with RNA-Seq.


  • An Illumina-Demonstrated Method for Sequencing the Complete Transcriptome –  Session will introduce an improved solution for the reduction of abundant transcripts in RNA-Seq experiments, based on an Illumina-optimized protocol utilizing duplex-specific nuclease (DSN) from Evrogen. Illumina scientists will provide a brief overview of DSN, will describe the enhancements made to the DSN workflow to optimize its performance for Illumina RNA-Seq, and will demonstrate its utility in a wide range of applications, including ncRNA discovery and FFPE transcriptome profiling.

RNA-Seq Data Analysis Tools

  • rQuant.web – is a web service to provide convenient access to tools for the quantitative analysis of RNA-Seq data. It allows to determine abundances of multiple transcripts per gene locus from RNA-Seq measurements. rQuant.web is available free of charge, to all users as a tool in a Galaxy installation. 
  • Scripture – is a method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio.
  • Cufflinks – assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.
  • SpliceMap – SpliceMap is a de novo splice junction discovery tool. It offers high sensitivity and support for arbitrarily long RNA-seq read lengths.
  • TopHat – is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
  • PALMapper – a combination of the spliced alignment method QPALMA with the short read alignment tool GenomeMapper. The resulting method, called PALMapper, efficiently computes both spliced and unspliced alignments at high accuracy while taking advantage of base quality information and splice site predictions.
  • RNA-MATE – A recursive mapping strategy for high-throughput RNA-sequencing data.
  • ERANGE – Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq
  • SeqMap – A Tool For Mapping Millions Of Short Sequences To The Genome.
  • Bioconductor – Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data.
  • BWA – BWA is a fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (targe), such as the human reference genome.
  • CisGenome – An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis.
  • GenePattern – is a powerful genomic analysis platform that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.
  • Galaxy – Mapping pipeline for Illumina, 454, and SOLiD sequencing data.
  • MAQ – stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences.
  • UCSC Genome Browser – This site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides portals to the ENCODE and Neandertal projects.