{"repo":"nf-core/dualrnaseq","free":true,"listed":false,"github":"https://github.com/nf-core/dualrnaseq","clone":"git clone https://github.com/nf-core/dualrnaseq.git","description":"Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.","language":"Nextflow","stars":25,"topics":["rna-seq","dualrna-seq","host-pathogen","readmapping","quantification","nextflow","pipeline","workflow","nf-core"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Dual RNA-seq pipeline nf-core/dualrnaseq is a bioinformatics pipeline built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible. Introduction nf-core/dualrnaseq is specifically used for the analysis of Dual RNA-seq data, interrogating host-pathogen interactions through simultaneous RNA-seq. This pipeline has been initially tested with eukaryotic host's including Human and Mouse, and pathogens including Salmonella enterica , Orientia tsutsugamushi , Streptococcus penumoniae , Escherichia coli and Mycobacterium leprae . The workflow should work with any eukaryotic and bacterial organisms with an available reference genome and annotation. Method The workflow merges host and pathogen genome annotations taking into account differences in annotation conventions, then processes raw data from FastQ inputs (FastQC, BBDuk), quantifies gene expression (STAR and HTSeq; STAR, Salmon and tximport; or Salmon in quasimapping mode and tximport), and summarises the results (MultiQC), as well as generating a number of custom summary plots and separate results tables for the pathogen and host. See the output documentation for more details. Workflow The workflow diagram below gives a simplified visual overview of how dualrnaseq has been designed. Documentation The nf-core/dualrnaseq pipeline comes with documentation about the pipeline, found in th","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/dualrnaseq/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}