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.
Average per sample
Average per study
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.
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.
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.
Get instant assistance for any issue from our extended and experienced bioinformatics team through dedicated slack channels, emails, or conference calls.
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.
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.
Montse’s investigation revolves around a topic that is intriguing and exciting: Aging. She has dedicated her postdoctoral efforts to study the process of aging, the factors that promote premature senescence as well as the mechanisms that may increase...