RNA-Seq Expression analysis

RNA Sequencing (RNA-Seq) is a revolutionary technique for transcriptome-wide analysis of gene expression. Given its high accuracy and sensitivity for measuring expression, it has become the standard for studying transcriptomic dynamics and identifying differences in expression between tissues, physiological stages, diseases and a wide range of other experimental designs.

Differential Expression and Gene Enrichment Pipeline

A workflow designed to test for quantitative changes in expression levels between experimental groups, and identify enriched pathways and ontology terms. This versatile workflow can be used for the analysis of any species with a published reference transcriptome (human, mouse, yeast, etc). All the steps in the pipeline are based on open source reference bioinformatics tools, considered as standards for RNA-Seq differential Expression Analysis.

  • FastQC: Quality controls of reads

  • Trimmomatic: Trimming of unwanted sequences

  • STAR: Splice-aware RNA read alignment

  • QualiMap2: Quality controls for read alignments

  • HTSeq: Read count of genomic features

  • DESeq2: Test for differential expression

  • fgsea: Gene Ontology and Pathway enrichment


All results are integrated in a single interactive report with tables and plots for each step performed by the pipeline.

Quality control metrics for sequence reads

Read alignment statistics

Principal component analysis

Multivariate data analysis

Differential expression

Pathway and Gene Ontology enrichment

  • Price: $13.5

    Average per sample

  • Runtime: 5 hrs

    Average per study

Why BatchX

BatchX offers a serverless infrastructure for running bioinformatics analyses as a fully managed service. With the click of a button, off-load all your complex processing requirements to the cloud in a cost-effective, secure, and scalable way.

Take full control of your analysis

Our RNA-Seq pipeline gives you the flexibility to customize it to suit your needs. It's super easy to change any parameter and re-run the analysis with the click of a button.

Bioinformatics analysis made easy

Our no code environment gives you the freedom you need to run the RNA-Seq pipeline with zero coding required. Share your results with collaborators in a secure and private manner.

Custom support

Get instant assistance for any issue from our extended and experienced bioinformatics team through dedicated slack channels, emails, or conference calls.

Our users love us

BatchX allows us to carry out the metagenomic analyses we need quickly and efficiently. The platform’s flexibility and the availability of the team allowed us to improve and adapt the workflows to meet our needs. As a rookie in bionformatics, BatchX is a source of inspiration, showing me how far bioinformatic analyses can go.

Ignacio Montero

Bioinformatician, Microviable Therapeutics

BatchX is super easy to use. Any bioinformatician who deals with complex pipelines including 16S will appreciate the efficiency – import scripts once and never worry about recurring errors. We also enjoyed per job cost updates.

Adrian Santiago Ortiz

Bioinformatician, IMOMA

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