RNA-Seq

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The bioinformatics applications assigned the Biological domain RNA-Seq ([ ]) are tabulated below.

Definition:

Synonyms:

Query returned 50 results.

	Biological domain	Bioinformatics method	Input format	Output format
ArrayExpressHTS	RNA-Seq RNA-Seq quantification		FASTQ
Avadis NGS	ChIP-seq RNA-Seq Sequencing DNA-Seq Small RNA-Seq RNA Methyl-Seq MeDIP-Seq Pathway or network analysis	Sequence alignment Visualisation Sequencing quality control Sequence analysis Analysis Biological interpretation	FASTA FASTQ SAM BAM ELAND BED Unaligned BAM	HTML VCF Tab-delimited Tab separated .txt TSV
Chipster	DNA methylation ChIP-seq RNA-Seq Immunoprecipitation experiment	Read mapping Peak calling Sequence motif recognition Genome visualisation Sequencing quality control Differential expression analysis Sequence trimming Pathway or network analysis Methylation analysis	FASTQ SAM BAM BED GTF	FASTQ SAM BAM BED GTF
CLCbio Genomics Workbench	Sequence assembly (de novo assembly) Whole genome resequencing Genomics Transcriptomics ChIP-seq SNP detection Indel detection RNA-Seq Regulatory RNA Mapping	Sequence assembly Sequence assembly (de-novo assembly) Read mapping Sequence alignment Ab-initio gene prediction Adapter removal Annotation Bisulfite mapping SNP calling Heat map generation Sequence assembly validation	FASTA FASTQ SAM BAM CSFASTA/CSQUAL (ABI SOLiD) ELAND GenBank Illumina Bustard	FASTA FASTQ SAM BAM GFF GenBank ACE Nexus CSV PDF XLS
ConDeTri	Genomics RNA-Seq Sequencing	Sequence trimming	FASTQ	FASTQ
Cufflinks	Transcriptomics RNA-Seq alignment RNA-Seq RNA-Seq quantification Alternative splicing	Read mapping Transcriptome assembly Differential expression analysis	SAM	GTF
DeFuse	RNA-Seq Gene structure		FASTQ
DSGseq	RNA-Seq Alternative splicing Gene expression	Statistical calculation Differential expression analysis RNA-Seq analysis	Table with count data SAM/BAM	Delimited Text
EdgeR	DNA methylation ChIP-seq RNA-Seq RNA-Seq quantification Gene expression analysis	Statistical calculation	Table with count data	Table
ESTcalc	RNA-Seq
Flux	RNA-Seq	Modelling and simulation
FrameDP	RNA-Seq
FusionCatcher	RNA-Seq Gene structure	Sequence alignment	FASTQ (Compressed) FASTQ SRA	Text
FusionHunter	RNA-Seq		FASTQ
FusionSeq	RNA-Seq Gene structure	Sequence alignment analysis	MRF	GFR BP
GENE-Counter	RNA-Seq		FASTA
Genedata Expressionist	Genomics Transcriptomics DNA methylation ChIP-seq SNP detection Indel detection RNA-Seq Sequencing Laboratory information management Copy number estimation Epigenetics Gene structure	Read mapping Sequence alignment Annotation Bisulfite mapping Clustering Genome visualisation Sequencing quality control Sequence analysis Statistical calculation Gene expression analysis RNA-Seq analysis	FASTA FASTQ QSEQ SAM BAM GFF BED VCF GTF BedGraph 2bit Nib GDC And many others.
Geneious	Sequence assembly (de novo assembly) Genomics RNA-Seq Metagenomics Epigenomics Structural variation Sequence analysis Phylogenetics Population genetics	Sequence assembly Read mapping Sequence alignment Visualisation Annotation Sequence assembly validation Genome visualisation Variant calling DNA barcoding Sequence motif discovery	FASTA FASTQ SAM ELAND GenBank CSFASTA CSQUAL
GeneProf	ChIP-seq RNA-Seq	Read mapping Visualisation Peak calling Sequencing quality control Differential expression analysis	FASTA (Compressed) FASTQ Others (Compressed) FASTA Table with count data Tab-delimited	FASTA FASTQ BED WIG XLS TXT HTML Tab-delimited Images
Genomatix Mining Station (GMS)	ChIP-seq SNP detection RNA-Seq	Sequence assembly Read mapping SNP calling Correlation	FASTA FASTQ GenBank EMBL Solexa Solexa with Probability	FASTA SAM BAM BED GAF
GenomicTools	Genomics ChIP-seq RNA-Seq	Peak calling Heat map generation Genome comparison	GFF BED SAM/BAM	SAM GFF BED
GenoMiner	Sequence assembly Sequence assembly (de novo assembly) ChIP-seq RNA-Seq	Sequence assembly Sequence alignment Peak calling Sequence error correction Plotting and rendering Mutation detection Gene expression profiling
GlobalSeq	RNA-Seq ChIP-Seq MicroRNA-Seq Meth-Seq	Omnibus test Global test Joint significance test
Goby framework	RNA-Seq	File reformatting
HeliSphere	Whole genome resequencing Genomics SNP detection RNA-Seq	Mapping	SMS	FASTA FASTQ SAM BAM BED WIG
Inchworm	Sequence assembly (de-novo assembly) RNA-Seq Transcriptome assembly
IOmics	Genomics Transcriptomics ChIP-seq RNA-Seq Regulatory RNA Exome capture Epigenomics	Sequence assembly Sequence alignment Ab-initio gene prediction Variant calling MiRNA analysis Exome analysis
MAYDAY	RNA-Seq	Visualisation
MeV	RNA-Seq	Visualisation Differential expression analysis Sequence clustering Classification
MISO	RNA-Seq RNA-Seq quantification Alternative splicing		SAM/BAM
MochiView	Genomics ChIP-seq RNA-Seq ChIP-on-chip Sequence motifs	Genome visualisation Sequence motif comparison	FASTA GFF BED WIG Custom MEME Bioprospector Custom Motif format	Varied
OLego	Genomics RNA-Seq alignment RNA-Seq	Read mapping Sequence alignment	FASTA FASTQ	SAM BED
PanGEA	SNP detection RNA-Seq DNA transcription
Pipeline Pilot	Sequence assembly (de novo assembly) Whole genome resequencing Genomics ChIP-seq SNP detection RNA-Seq Sequence analysis Gene expression analysis Next Generation Sequencing	Read mapping Sequence alignment Sequence analysis Variant calling Comparative genomics Gene expression analysis	Velvet MUMmer Bowtie CisGenome MACS TopHat SAMtools BWA GATK Cufflinks Tablet BLAST MUSCLE BreakDancerMax CNV-seq FASTQC Integrative Genomics Viewer Mapreads MIRA3 SnpEff Tabix Artemis BioJava BioPerl ClustalW EMBOSS HMMER Jalview Primer3 PROSITE Sim4	Circos GBrowse2
QSeq	ChIP-seq RNA-Seq Regulatory RNA	Sequence alignment Visualisation Peak calling
RDiff	Transcriptomics RNA-Seq Alternative splicing	Sequence alignment Differential expression analysis	SAM BAM GFF3	Tab-delimited file
RobiNA	RNA-Seq	Differential expression analysis	FASTQ
S-MART	ChIP-seq RNA-Seq		FASTA FASTQ MAQ SOAP PSL SEQMAP	TXT GFF3
Samscope	Genomics ChIP-seq RNA-Seq	Read mapping Visualisation	GFF BED WIG CSV GTF SAM/BAM BEDGraph	BIP
SeqGSEA	Genomics RNA-Seq Biomedical Sciences	Statistical calculation Functional enrichment Functional analysis	SAM BAM	Tab separated
SeqSaw	RNA-Seq Alternative splicing	Read mapping Sequence alignment	FASTA	SAM BED
SeqSolve	Transcriptomics ChIP-seq RNA-Seq Alternative splicing	Ab-initio gene prediction Differential expression analysis Quality control	SAM BAM GFF BED TXT GTF	BED PDF XLS TXT JPG PPT
Skewer	Sequence assembly RNA-Seq Small RNA Sequencing	Read mapping Adapter removal Sequence trimming Read pre-processing	(Compressed) FASTQ (Compressed) FASTA	Fasta.gz Fastq.gz Fasta/q
SOAPfusion	Transcriptomics RNA-Seq Gene structure		FASTQ	Delimited Text
SpliceTrap	RNA-Seq RNA-Seq quantification Alternative splicing	Statistical calculation	FASTA FASTQ	TXT
SplicingViewer	Genomics RNA-Seq	Mapping	SAM/BAM	GFF Tab
STAR	Transcriptomics RNA-Seq	Sequence alignment	FASTA FASTQ	SAM
Syapse	Genomics Transcriptomics DNA methylation ChIP-seq SNP detection Indel detection RNA-Seq Metagenomics DNA transcription Epigenomics Structural variation Population genetics Comparative genomics DNA-Seq Regulatory genomics	Visualisation Sequence analysis Differential expression analysis Ontology comparison Exome analysis Variant classification	VCF
Trans-ABySS	SNP detection Indel detection RNA-Seq Gene structure		FASTQ ABySS assemblies
UnoSeq	Sequence assembly (de-novo assembly) RNA-Seq Transcriptome assembly