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NewSpatial Transcriptomics Pipeline with Spotty

Spatial Transcriptomics is a method that allows visualization and quantitative analysis of the transcriptome in individual tissue sections. Spatial Transcriptomics Pipeline with Spotty is a workflow for processing raw sequence data (paired FASTQ-files) generated using the Spatial Transcriptomics technology. The workflow produces a table of spatially distributed gene counts for downstream analysis.

This workflow consists of two nested workflows:

  1. ST Pipeline which performs demultiplexing and decoding of the RNA-Seq reads.
  2. The Spotty workflow with post processing, to perform automatic spot identification and pairing between the fluorescent (Cy3) and tissue (HE) image. Spotty is proprietary and available only on the Seven Bridges platform environments.

Read more about the workflow on our blog.

NewData Cruncher Interactive Analyses – Public project

As a part of the effort to grow a comprehensive set of platform features and capabilities, we have developed several Data Cruncher Interactive Analyses as an additional resource that should help users mitigate challenges related to interpretation of data obtained through secondary analysis. These Data Cruncher analyses can be found in the Data Cruncher Interactive Analyses public project.

The project contains five analyses:

  • Ballgown Interactive Analysis
  • VCF visualization Interactive Analysis
  • Structural variation Interactive Analysis
  • ChIP-seq Interactive Analysis
  • Microbiome Differential Abundance Analysis

Each Interactive Analysis comes with explanations of analysis steps and a corresponding set of files needed for successful execution.

NewSupported instances update

The new generation of AWS EC2 Compute Optimized instances (C5) and General Purpose instances (M5) is now also available in task executions and Data Cruncher analyses on See the full list of supported AWS EU instances in our documentation.