RNA-RNA interactome analysis using ChiRA tool suite

Associated Tutorial

This workflows is part of the tutorial RNA-RNA interactome data analysis - chira v1.4.3, available in the GTN

Features

• Includes Galaxy Workflow Tests

Thanks to...

**Tutorial ...

GATK4 RNA variant calling pipeline

Nextflow rnafusion analysis pipeline, part of the nf-core community.

Precision HLA typing from next-generation sequencing data.

Precision HLA typing from next-generation sequencing data using OptiType.

Table of Contents

Introduction Quick Start

With Docker With Singularity

Documentation Pipeline DAG

Input fastq Input bam

Credits

Introduction

OptiType is a HLA genotyping algorithm based on integer linear programming. Reads of whole exome/genome/transcriptome sequencing data are mapped against a reference of known MHC class I alleles. To produce accurate 4-digit HLA genotyping predictions, all major and minor HLA-I loci are ...

nf-core/cageseq

CAGE-seq pipeline.

Introduction

UNDER DEVELOPMENT

This pipeline is currenlty under development. The workflow is not yet finished.

nf-core/cageseq is a pipeline built for the analysis of CAGE-sequencing data.

Analysis steps consist of adapter and artefact trimming (cuatadapt), alignment to a reference (STAR) and CAGE tag counting. Additionally, several quality control steps (FastQC, MultiQC) are included to allow for easy verification of results after a run.

The pipeline is built ...