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