RNA sequencing data analysis bioinformatics software tools

RNA sequencing (RNA-seq) also known as whole transcriptome shotgun sequencing (WTSS) is the next-generation sequencing technology to study the transcriptome. It could be used as an alternative to microarrays for gene expression analysis, without the need to know the RNA sequence…

RNA-seq analysis steps

Preprocessing & quality control

Data analysis

Annotation & interpretation

File, data & workflows

RNA-seq analysis workflow

Click the icons of the schema to view tools

RNA-seq analysis workflow schema

RNA sequencing data analysis bioinformatics software tools

Most Recent Tools

G T A T C G C T A
IsoformSwitchAn…
Desktop

IsoformSwitchAnalyzeR

Identifies and analysis the potential consequences of isoform switches from…

Identifies and analysis the potential consequences of isoform switches from RNA-seq derived quantification of both novel and annotated full-length isoforms. IsoformSwitchAnalyzeR is an easy to use R…

G T A T C G C T A
GigaTON
Dataset

GigaTON Gigas TranscriptOme pipeliNe

Studies the genome of the Pacific oyster, Crassostrea gigas. GigaTON provides a…

Studies the genome of the Pacific oyster, Crassostrea gigas. GigaTON provides a web browser that allows a convenient view of the target contig counterparts in numerous other databases at a single…

G T A T C G C T A
COSINE
Desktop

COSINE

Aligns long sequences with high variations or errors including insertions and…

Aligns long sequences with high variations or errors including insertions and deletions to the target. COSINE has a predictable computational resource usage for mapping reads from E. coli genome, S.…

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Dynamic-BM
Dataset

Dynamic-BM Dynamic-BodyMap

Allows to find data about temporal gene expression profiles. The Dynamic-BM…

Allows to find data about temporal gene expression profiles. The Dynamic-BM interface is design in order to simplify the utilization by users for browsing and searching the dynamic expression pattern…

Most Popular Tools

G T A T C G C T A
SAMtools
Desktop

SAMtools

A suite of programs for interacting with high-throughput sequencing data. It…

A suite of programs for interacting with high-throughput sequencing data. It can manipulate alignments in the SAM/BAM/CRAM formats : reading, writing, editing, indexing, viewing and converting…

G T A T C G C T A
Bowtie
Desktop

Bowtie

An ultrafast, memory-efficient short read aligner. It aligns short DNA…

An ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a…

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AlienTrimmer
Desktop

AlienTrimmer

Detects and removes multiple alien sequences in both ends of sequence reads.…

Detects and removes multiple alien sequences in both ends of sequence reads. Based on the decomposition of specified alien nucleotide sequences into k-mers, AlienTrimmer is able to determine whether…

G T A T C G C T A
Trim Galore!
Desktop

Trim Galore!

A wrapper tool around Cutadapt and FastQC to consistently apply quality and…

A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation…

Curators for RNA-seq analysis

  • Rekin's Janky's avatar image
    Rekin's Janky
    Laboratory of Computational…
  • Bogdan Mirauta's avatar image
    Bogdan Mirauta
    Laboratory of Computational and…
  • Mikhail Shugay's avatar image
    Mikhail Shugay
    Genomics of Adaptive Immunity Lab,…
  • Abdoulaye Baniré Diallo's avatar image
    Abdoulaye Baniré Diallo
    Department of Computer Sciences,…
  • Antoine Rousselin's avatar image Antoine Rousselin's country flag
    Antoine Rousselin
    Centre François Baclesse

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