RNA-Seq Structural alteration analysis

RNA sequencing (RNA-Seq) represents the most precise approach for the characterization of transcript isoforms both known and novel. Compared to previous techniques, RNA-Seq does not require designing probes for selected candidate genes, making it an effective method to explore the full transcriptome and reveal novel transcripts, alternatively spliced genes and other structural rearrangements such as gene fusions.

Structural alterations pipeline

A workflow designed to identify transcriptional structural rearrangements such as gene fusions, viral integration sites and gene truncations as well as alternative splicing events due to intron retention, exon skipping and alternative use of splicing sites. 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 Structural alteration analysis.

  • FastQC: Quality controls of reads

  • STAR-Fusion: Identify fusion transcripts

  • Arriba: Identify structural rearrangements

  • QualiMap2: Quality controls for read alignments

  • karyoploteR: Read distribution ideograms

  • asgal: Detect transcriptional alternative events

  • DEXSeq: Differential exon usage

  • SPLICE-q: Splicing efficiency quantification


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

Read distribution ideograms

Structural rearrangements

Alternative splicing events

Differential exon usage

  • Price: $30

    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 has provided me with the autonomy I needed. I can now easily and rapidly perform analysis and review results. I know I can rely on their bioinformatics expertise when I need to. I feel I’m now more in control of my research studies.

Alberto Gonzalez

Researcher, VHIO

We were yearning for independence and shorter turnaround times. With BatchX we can decide when and how we perform our bioinformatics analysis and have our results instantly. Thank you, guys, for the support and for the platform! I now feel I have bioinformatics super powers!

Montse Vega

Researcher, Pompeu Fabra University

BatchX User Insights: Montse Vega

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...