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bter_neonicotinoid_exposure_experiment

Caste- and pesticide-specific effects of neonicotinoid pesticide exposure on gene expression in bumblebees

https://github.com/wurmlab/bter_neonicotinoid_exposure_experiment

Science Score: 57.0%

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Repository

Caste- and pesticide-specific effects of neonicotinoid pesticide exposure on gene expression in bumblebees

Basic Info
  • Host: GitHub
  • Owner: wurmlab
  • License: gpl-3.0
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 1010 KB
Statistics
  • Stars: 7
  • Watchers: 7
  • Forks: 2
  • Open Issues: 0
  • Releases: 0
Created almost 8 years ago · Last pushed almost 7 years ago
Metadata Files
Readme License Citation

README.md

Context & citation

This repository contains all scripts used for the differential expression analysis of Bombus terrestris workers and queens in response to neonicotinoid exposure. This was developed as part of a NERC-funded project reported implemented in Yannick Wurm's lab at Queen Mary University of London. Findings are reported in the following manuscript:

Colgan, T.J., Fletcher, I.K., Arce, A.N., Gill, R.J., Ramos Rodrigues, A., Stolle, E., Chittka, L. and Wurm, Y.
Caste- and pesticide-specific effects of neonicotinoid pesticide exposure on gene expression in bumblebees. Molecular Ecology (2019).

License

This work is distributed under the GPLv3 license. Reuse of code derived from this repository is permitted under two conditions: 1) Proper attribution (i.e., citation of the associated publication; see CITATION.cff and above). 2) Publication of reused scripts on an open-access platform, such as Github.

Workflow

Analysis workflow consisted of:
1. Quality assessment of aligned data using multiQC.
2. Pseudoalignment and transcript quantification using kallisto.
3. Splice-aware alignment using HISAT2.
4. Exon-level read count generation using HTSeq.
5. Differential expression analysis using DESeq2.
6. Differential exon usage analysis using DEXSeq.
7. Gene Ontology enrichment analysis using topGO.
8. Comparative analysis of read counts generated by kallisto and HTSeq.
9. Generation of graphics for visualisation of results.

Repository contents:

01_multiqc_quality_assessment |- hisat2_to_multiQC.sh 02_amplitude_kallisto_quantifications/ |- run_kallisto.sh 03_spliced_mapping_hisat |- hisat_mapping.sh 04_exon_level_read_count_quantifications |- prepare_input_files_for_dexseq.sh 05_differential_expression_analysis |- treatment_caste_group_analysis |- |- gene_level_group_analysis.Rmd |- treatment_caste_interaction_analysis |- |- gene_level_3_treatments.Rmd |- |- input |- |- |- sample_information.txt |- treatment_specific_analysis |- |- gene_level_3_treatments.Rmd |- |- input |- |- |- sample_information.txt 06_differential_exon_usage_analysis |- dexseq_analysis.Rmd |- get_lowest_exon_p_value.sh 07_gene_ontology_enrichment_analysis |- go_enrichment_analysis.Rmd |- input |- |- dmel_vs_bter_biomart.input_for_converter.output.txt 08_comparative_read_count_analysis |- compare_kallisto_hisat2_quants.Rmd 09_plot_visualisation |- euler_diagram.Rmd |- plot_DEGs_heatmap.Rmd |- plot_go_barchart.Rmd utility |- barchart_helper_functions.R |- description_from_LOCid.R |- helper_functions_for_heatmaps.R

Owner

  • Name: Yannick Wurm research lab @ QMUL & Turing
  • Login: wurmlab
  • Kind: organization
  • Location: Queen Mary University of London

Ants, bees, evolutionary genomics & bioinformatics.

Citation (CITATION.cff) 

cff-version: 1.0.3
message: If you use this software, please cite it as below.
authors:
  - family-names: Colgan; Fletcher; Arce; Gill; Ramos-Rodrigues; Stolle; Chittka; Wurm 
    given-names: Thomas J.; Isabel K.; Andres N.; Richard J.; Ana; Eckart; Lars; Yannick
    orcid: (Thomas Colgan) https://orcid.org/0000-0002-0547-8228; (Yannick Wurm) https://orcid.org/0000-0002-3140-2809
title: Caste- and pesticide-specific effects of neonicotinoid pesticide exposure on gene expression in bumblebees.
journal: Molecular Ecology
doi: 10.1111/mec.15047
date-released: 2018-12-17
license: GPLv3
repository: https://github.com/wurmlab/Bter_neonicotinoid_exposure_experiment

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