References and test datasets for the Cactus pipeline
type: Dataset
distribution: Landing page for the dataset
description: Overview This item contains references and test datasets for the Cactus pipeline. Cactus (Chromatin ACcessibility and Transcriptomics Unification Software) is an mRNA-Seq and ATAC-Seq analysis pipeline that aims to provide advanced molecular insights on the conditions under study. Test datasets The test datasets contain all data needed to run Cactus in each of the 4 supported organisms. This include ATAC-Seq and mRNA-Seq data (*.fastq.gz), parameter files (*.yml) and design files (*.tsv). They were were created for each species by downloading publicly available datasets with fetchngs (Ewels et al., 2020) and subsampling reads to the minimum required to have enough DAS (Differential Analysis Subsets) for enrichment analysis. Datasets downloaded: - Worm and Humans: GSE98758 - Fly: GSE149339 - Mouse: GSE193393 References One of the goals of Cactus is to make the analysis as simple and fast as possible for the user while providing detailed insights on molecular mechanisms. This is achieved by parsing all needed references for the 4 ENCODE (Dunham et al., 2012; Stamatoyannopoulos et al., 2012; Luo et al., 2020) and modENCODE (THE MODENCODE CONSORTIUM et al., 2010; Gerstein et al., 2010) organisms (human, M. musculus, D. melanogaster and C. elegans). This parsing step was done with a Nextflow pipeline with most tools encapsulated within containers for improved efficiency and reproducibility and to allow the creation of customized references. Genomic sequences and annotations were downloaded from Ensembl (Cunningham et al., 2022). The ENCODE API (Luo et al., 2020) was used to download the CHIP-Seq profiles of 2,714 Transcription Factors (TFs) (Landt et al., 2012; Boyle et al., 2014) and chromatin states in the form of 899 ChromHMM profiles (Boix et al., 2021; van der Velde et al., 2021) and 6 HiHMM profiles (Ho et al., 2014). Slim annotations (cell, organ, development, and system) were parsed and used to create groups of CHIP-Seq profiles that share the same annotations, a…
modified: 2023-05-30T00:00:00Z
issued: 2022-12-21T00:00:00Z
publisher: Karolinska Institutet
theme: HEAL
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Jerome Salignon
    type: Agent
    account: https://orcid.org/0000-0002-7242-3817
    type: PrivateIndividual(s)
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Lluis Milan Arino
    type: Agent
    type: PrivateIndividual(s)
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Maxime Garcia
    type: Agent
    account: https://orcid.org/0000-0003-2827-9261
    type: PrivateIndividual(s)
qualified attribution: Attribution
  had role: principalInvestigator
  agent: Christian Riedel
    type: Agent
    account: https://orcid.org/0000-0002-3689-8022
    type: PrivateIndividual(s)
keyword: Bioinformatic methods development
keyword: Genomics and transcriptomics

Landing page for the dataset
type: Distribution
title: Landningssida för datasetet @sv
access URL: References and test datasets for the Cactus pipeline
availability: stable

Karolinska Institutet
type: Agent
type: Academia-ScientificOrganisation
source: https://ror.org/056d84691