Discussion Forums

RNA-Seq Data Analysis Tools

  • Myrna – a cloud computing tool for RNA sequence analysis – The new software calculates differential gene expression in large RNA-seq datasets by using Bowtie, an ultrafast, memory-efficient short read aligner, and R/Bioconductor for statistical calculations. These tools are combined in an automatic, parallel pipeline that runs in the cloud using Elastic MapReduce, on a local Hadoop cluster.
  • MapSplice – Splice Junction Mapping Tool – a second generation splice detection algorithm, MapSplice, whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency.
  • Oqtans: Online Quantitative Transcriptome Analysis – for quantitatively analyzing RNA-Seq experiments. It is based on the Galaxy-framework and provides tools for read mapping, transcript reconstruction and quantitation.
  • DESeq – Digital gene expresion analysis based on the negative binomial distribution – an error model that uses the negative binomial distribution, with variance and mean linked by local regression, to model the null distribution of the count data. The method controls type-I error and provides good detection power.
  • MapPER – an RNA-seq paired-end read (PER) protocol – samples transcript fragments longer than the sequencing capability of today’s technology by sequencing just the two ends of each fragment. Deep sampling of the transcriptome using the PER protocol presents the opportunity to reconstruct the unsequenced portion of each transcript fragment using end reads from overlapping PERs, guided by the expected length of the fragment.
  • 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.
  • 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.