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This repository contains all scripts used for the differential expression analysis ofBombus terrestris workers and queens in response to neonicotinoid exposure. This was developed as part of a NERC-funded project reported implemented inYannick 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).

This work is distributed under theGPLv3 license. Reuse of code derived from this repository is permitted under two conditions:

1. Proper attribution (i.e., citation of the associated publication; seeCITATION.cff and above).
2. Publication of reused scripts on an open-access platform, such as Github.

Analysis workflow consisted of:

1. Quality assessment of aligned data usingmultiQC.
2. Pseudoalignment and transcript quantification usingkallisto.
3. Splice-aware alignment usingHISAT2.
4. Exon-level read count generation usingHTSeq.
5. Differential expression analysis usingDESeq2.
6. Differential exon usage analysis usingDEXSeq.
7. Gene Ontology enrichment analysis usingtopGO.
8. Comparative analysis of read counts generated by kallisto and HTSeq.
9. Generation of graphics for visualisation of results.

01_multiqc_quality_assessment|- hisat2_to_multiQC.sh02_amplitude_kallisto_quantifications/|- run_kallisto.sh03_spliced_mapping_hisat|- hisat_mapping.sh04_exon_level_read_count_quantifications|- prepare_input_files_for_dexseq.sh05_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.txt06_differential_exon_usage_analysis|- dexseq_analysis.Rmd|- get_lowest_exon_p_value.sh07_gene_ontology_enrichment_analysis|- go_enrichment_analysis.Rmd|- input|- |- dmel_vs_bter_biomart.input_for_converter.output.txt08_comparative_read_count_analysis|- compare_kallisto_hisat2_quants.Rmd09_plot_visualisation|- euler_diagram.Rmd|- plot_DEGs_heatmap.Rmd|- plot_go_barchart.Rmdutility|- barchart_helper_functions.R|- description_from_LOCid.R|- helper_functions_for_heatmaps.R