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Jeanie Lim edited this page Jun 24, 2016 · 1 revision

Comprehensive (but not exhaustive) table of tools for RNA-seq analysis

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####Supplementary Table 2. Tools for RNA-seq analysis (Griffith et al. 2015)

All tools used in the online tutorial (www.rnaseq.wiki) are referenced below (in bold) along with alternative tools in each category. Where possible a citation is provided. Links are also provided to help the user evaluate the code and the level of maintenance. Where possible the link goes directly to a source controlled repository such as a git repo. Additional lists of tools can be found here: Alamancos et al. (arXiv), Hooper et al. [24447644], the rna-seqblog, and RNA-seq - Protocols and Algorithms. This table is meant to be comprehensive but not exhaustive. Some RNA-seq analysis applications that are not explicitly covered here include co-regulation (co-expression), disease classification, time series, expression compendium databases, outlier expression, data normalization, and miRNA analysis.

Category Representative tools
Raw data QC [25577376, 25150838] FastQC, HTQC [23363224], QC3 [24703969], kPAL [25514851].
Read trimming [24376861] Trimmomatic [24695404], Skewer [24925680], Flexbar [24832523], FASTX.
Alignment (splice aware, for alignment to a reference genome) [24185836] TopHat [19289445, 23618408], STAR [23104886], HISAT [25751142], HISAT2, segemehl [24512684], SubRead, GSNAP, MapSplice [20802226], JAGuaR [25062255], SpliceMap [20371516], HMMSplicer [21079731], TrueSight/UnSplicer [24259430].
Alignment (non splice aware for alignment to a reference transcriptome) [23060614, 23758764] BowTie [19261174], Bwa [19451168].
Post-alignment QC [24185836] FastQC, samtools [19505943], QuaCRS [25368506], RSeQC [22743226], RNA-SeQC [22539670], Picard CollectRnaSeqMetrics, BAMstats, SAMstat [21088025], BlackOPs [23935067], seqbias [22285831].
Gene/transcriptome annotation [24722185, 25319663] Annocript [25701574], XSAnno [24884593], GeneMark-ET [24990371], WImpiBLAST [24979410], RNASEG [24780064], TSSAR [24674136], Vicinal [24623808], OMIGA [24609470], CoRAL [24145223], AfterParty [24093729], ShortStack [23610128], CIRI [25583365].
Small RNA identification and characterization (e.g., miRNAs) [25319663, 23720668] ShortStack [23610128], CoRAL [24145223], MTide [25256573], FlaiMapper [25338717], miRPlant [25117656], PROmiRNA [23958307], omiRas [23946503], DREAM [25840043].
Transcript assembly (reference genome guided) [24185837, 21897427, 23393030] Cufflinks [20436464], Scripture [20436462], StringTie [25690850], bayesembler [25367074], IsoLasso [21951053].
Transcript assembly (de novo, reference genome free) [21897427, 23393030, 23056003, 23666209, 25084827, 25279728, 25788326] Trinity [23845962], Trans-ABySS [20935650], Oases [22368243], RSEM [21816040], DETONATE [25608678], SEECER (sequencing error correction for assembly) [23558750], BRANCH [23493323] uses partial or related genomics sequences as a guide, EBARDenovo [23457040], Bridger [25723335].
Transcript abundance or expression estimation (FPKM/RPKM) [24185837, 24885830, 24109770, 24685233] Cufflinks [20436464], eXpress [23160280], RSEM [21816040], Sailfish (alignment free) [24752080], RNA-Skim (alignment free) [24931995], MITIE [23980025], ireckon [23204306], DRUT [23202426], Kallisto (alignment free) [arXiv].
Obtaining raw transcript/gene read counts (FPM/RPM) [21176179] HTSeq [25260700], FeatureCounts [24227677], Rcount [25322836], maxcounts [24564404], FIXSEQ (adjusts counts to compensate for overdispersion) [24603409], Cuffquant.
Differential expression [25119138, 24300110, 24020486, 25024085] Cuffdiff [23222703], limma [25605792], DESeq2 [25516281], EdgeR [19910308], Corset (for de novo assembled transcriptomes) [25063469], sSeq [23589650], BADGE [25252852], compcodeR [24813215], metaRNASeq [24678608], Characteristic Direction [24650281], NPEBseq [23981227].
Alternative splicing, alternative expression [24447644, 24885830, 24058384, 24549677, 24951248, 25511303] Cuffdiff [23222703], DEXSeq [22722343], ALEXA-seq [20835245], IUTA [25283306], FineSplice [24574529], PennSeq [24362841], FlipFlop [24813214], SNPlice [25481010], spliceR [24655717], GESS [24447644], RNASeq-MATS [23872975], SplicingCompass [23449093], DiffSplice [23155066], SigFuge [25030904], SUPPA [bioRXiv], CLASS [bioRXiv], SplAdder [bioRXiv], SplicePie [25800735].
Variant (e.g., SNP) and mutation detection [23555596, 24075185, 22468815], germline or somatic, and eQTL/sQTL characterization [25733796] GATK (Best Practices Guide) [20644199], samtools [19505943], SNVMix [20130035], SNPlice [25481010], eSNV-detect [25352556], RVboost [25170027], sQTLseekeR [25140736], eQTL/ASE, [BioRXiv], SNiPloid [24163691], SNPiR [24075185], QualitySNPng [23632165], RNAmapper [23299976], CRAC [23537109], RADIA [25405470].
RNA editing [22327324, 23291724, 23598527, 25859542] REDItools [23742983], GIREMI [25730491], ICEBreaker [25855956].
Allele specific expression [23919664, 25183311, 25339465] AlleleSeq [21811232], Allim [23615333], mamba [25819081], EMASE, MBASED [25315065], limma [25605792].
Viral detection [23740984, 23279287, 22647373] VirusSeq [23162058], VirusFinder [23717618], RNA CoMPASS [24586784].
Fusion detection [25500544, 25266161, 23815381, 23555082, 25286921] FusionQ [23815381], TRUP [25650807], Dissect [22689759], Trans-ABySS [20935650], PRADA (RNA-seq pipeline with a fusion module) [24695405], Pegasus (used for fusion annotation) [25183062], FusionCatcher, ChimeraScan [21840877], TopHat-fusion [21835007], BreakFusion [22563071], deFuse [21625565], FusionHunter [21546395], EricScript [23093608], Barnacle [23941359], bellerophontes [22711792], Chimera (merge results from multiple fusion algorithms) [25286921], GFML (format for representing fusion data) [23072312].
Visualization [24792048, 25757788] SplicingViewer [22226708], IGV [22517427], Sashimi plots [25617416], IGB (splicing visualization protocol) [24792048], PrimerSeq (Visualize RNA-seq data for primer design) [24747190], ASTALAVISTA [25577392], Circos [19541911], Epiviz [25086505], RNAbrowse [24823498], ZENBU [24727769], RNAseqViewer [24215023], viRome [23709497], miRseqViewer [25322835], Circleator [25075113], RNASeqBrowser [25766521].
Integration of DNA-seq and RNA-seq data [23499923] Veridical [24741438], SpliceFinder [24498620], nFuse [22745232], RADIA [25405470].

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6-iii. Integrated assignment answers

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The Unix Shell Bootcamp

#Table of Contents

  1. Module 0 Setting Up for Data Analysis
    1. Introduction to High Performance Computing Cluster
    2. Connecting to MGHPCC
    3. Computing Environment
    4. Unix Tutorial Part 1: UNIX Bootcamp
    5. Unix Tutorial Part 2: Shell Scripting
    6. Unix Tutorial Practice
    7. Submitting computing jobs to HPC using LSF
    8. Ignore: Git Tutorial
  2. Module 1 Introduction/ Overview
    1. Overview of RNA-seq Experiment
    2. RNA-Seq Analysis Pipeline
    3. RNA-Seq Input Data
    4. RNA-seq File Formats and Software-Specific Files
    5. Getting Data for Analysis
  3. Module 2 Quality Control
    1. Data Quality Assessment
    2. Analyzing FastQC Report
    3. Adapter Removal, Trimming, and Filtering
  4. Module 3 Tuxedo Pipeline
    1. The Tuxedo Pipeline
    2. Read Alignment with TopHat2
    3. Transcript Assembly with Cufflinks
    4. Differential Analysis with Cuffdiff
    5. Visualization with CummeRbund
  5. Resources and Reference
    1. Resource: RNA-Seq Analysis Techniques
    2. Resource: Tools for RNA seq Analysis
    3. Resource: Concepts in sample preparation and library construction that can influence study design, analysis and interpretation
    4. Common RNA seq analysis questions and their answers
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