Workflows

This Galaxy workflow takes a list of tumor/normal sample pair variants in VCF format and

1. annotates them using the ENSEMBL Variant Effect Predictor and custom annotation data
2. turns the annotated VCF into a MAF file for import into cBioPortal
3. generates human-readable variant- and gene-centric reports

The input VCF is expected to encode somatic status, somatic p-value and germline p-value of each variant in varscan somatic format, i.e., via SS, SPV and GPV INFO keys, respectively.

We assume the identifiers of the input list are like: sample_name_replicateID. The identifiers of the output list will be: sample_name

Racon polish with long reads, x4

Downloads fastq files for sequencing run accessions provided in a text file using fasterq-dump. Creates one job per listed run accession.

This workflow takes as input SR BAM from ChIP-seq. It calls peaks on each replicate and intersect them. In parallel, each BAM is subsetted to smallest number of reads. Peaks are called using both subsets combined. Only peaks called using a combination of both subsets which have summits intersecting the intersection of both replicates will be kept.

Genome-wide alternative splicing analysis v.2

Abstract CWL Automatically generated from the Galaxy workflow file: Copy of Genome-wide alternative splicing analysis

This workflow correspond to the Genome-wide alternative splicing analysis training. It allows to analyze isoform switching by making use of IsoformSwitchAnalyzeR.

To discover causal mutations of inherited diseases it’s common practice to do a trio analysis. In a trio analysis DNA is sequenced of both the patient and parents. Using this method, it’s possible to identify multiple inheritance patterns. Some examples of these patterns are autosomal recessive, autosomal dominant, and de-novo variants, which are represented in the figure below. To elaborate, the most left tree shows an autosomal dominant inhertitance pattern where the offspring inherits a faulty ...

Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring