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This page contains links to all the exercises the Outreach team have available. You can use these to construct coursebooks for specific courses. Please note that Ensembl training materials are distributed under a Creative Commons BY license – you are required to credit Ensembl with the creation of these materials if you use them.

* Please note the release number in the 'Updated' column.  Some exercises are made to older Ensembl/Ensembl Genomes versions (releases) and may not work on the current site.  

The first table contains presentations with slides, followed by walkthroughs with screenshots, and questions and answers.

Use www.ensembl.org unless a non-vertebrate group is specified, in which case use www.ensemblgenomes.org.

Presentations


TopicVertebrates (or chordates)Non-vertebratesUpdatedAdded bySlides
Intro on accessing 1000s of genomes in EG
Bacteria22DeniseIntroduction to Ensembl Bacteria.pptx
Advances aspects of accessing 1000 genomes in EG
Bacteria22DeniseAdvanced Ensembl Bacteria.pptx


Walkthroughs (with screenshots)

TopicVertebrates (or chordates)Non-vertebrates?UpdatedAdded byWalkthrough
Basic browser walkthrough - ABCD1 geneHuman
76Giuliettawalk_through_browser_e76.docx
Basic browser walkthrough – OS01G0775500 gene
Plants (rice)EG35VictoriaRiD_riceOS01G0775500.docx
BioMart walkthrough - human genesHuman
84EmilyDemo BioMart
Browser walkthrough sir2 gene
Fungi (yeast)22Denisewalkthrough_yeast.docx
Browser walkthrough DREB gene
Plants (bread wheat)22Denisewalkthrough_wheat.docx
Browser walkthrough AP1 gene
Plants (Arabidopsis)25Denisewalkthrough_arabidopsis.docx
Finding species dataMultiAll84/31EmilySpecies_data
Region in detail viewHuman
84EmilyRegion_in_detail_walkthrough
Region in detail view—SHHHuman
89VictoriaRegion_in_detail_SHH
Gene and transcript tabsHuman
84EmilyGene_transcript_tabs_walkthrough
Gene and transcript tabs – OS01G0775500 gene
Plants (rice)EG35VictoriaG&T_riceOS01G0775500.docx
Gene and transcript tabs — SHHHuman
89VictoriaGenes and transcripts — SHH
Variation in the browserHuman
84Emilyvariation_in_the_browser_walkthrough
Variation in the browser – OS01G0775500 gene
Plants (rice)EG35Victoriavariation_riceOS01G0775500.docx
Variation in the browser – SHHHuman
89VictoriaVariation—SHH
VEP online tool with default formatHuman
84EmilyVEP_online_tool
Compara in the browserHuman
84Emilycompara_walkthrough
RegulationHuman
84Emilyregulation_walkthrough
Upload BED file to view in EnsemblHuman
84EmilyBED_upload
Attach BAM file to view in EnsemblHuman
84EmilyBAM_upload
Perform a REST API queryHuman
84EmilyREST_query
Browser, VEP and REST
Bacteria22Denisebrowser_VEP_Rest.docx
General walkthrough with Variation slantHuman
75Emilyvariation_browser.docx
BioMart with variation slantHuman
75Emilyvariation_biomart.docx
BioMart, variation: barley
Plants (barley)EG35Victoria
Region in detail view
Plants - wheat31Emilywheat_region
Gene and transcript tabs of a PHI-base annotated gene
Fungi - Zymoseptoria tritici31EmilyZT_phibase_gene
BioMart query with a wheat region
Plants - wheat31Emilywheat_biomart_demo
Variation in wheat
plants - wheat31Emilywheat_variation_demo
VEP in wheat
plants - wheat31Emilywheat_vep_demo
Whole genome alignments
plants - rice31Emilyrice_alignments_demo
 Gene trees and homologues
plants - wheat 31 Emily wheat_gene_trees_homologues
Uploading BED files
Fungi - Zymoseptoria tritici31Emilyfungi_bed
Attaching RNASeq files from the Track Hub Registry
plants - rice31EmilyRice_RNAseq_trackhub
Gene and transcript tabs
plants - barley30EmilyBarley_gene_demo
BioMart rice region
plants - rice30Emilyrice_biomart_demo
Variation in rice
plants - rice30Emilyrice_variation_demo
Region in cowlivestock - cow
83Emilycow_region_demo
Gene and transcript tabslivestock - pig
83Emilypig_gene_demo
BioMart sheep gene listlivestock - sheep
83Emilysheep_biomart_demo
Variationlivestock, bird - chicken
83Emilychicken_variation_demo
VEP with coordinateslivestock - sheep
83Emilysheep_vep_demo
Compara gene trees and homologueslivestock - cow
83Emilycow_genetrees_orthologues_demo
Compara alignmentslivestock - pig
83Emilypig_alignment_hoxD_demo
Region in detail
metazoa - Anopheles gambiae29EmilyRegion_mozzies
Gene and transcript tabszebrafish
82Emilyzebrafish_gene_demo
BioMart gene list
metazoa - Anopheles gambiae29Emilymozzie_biomart_demo
Variation in the browserzebrafish
82Emilyzebrafish_variation_demo
VEP coordinates
metazoa - Anopheles gambiae29Emilymozzie_VEP_demo
Gene trees and homologues
metazoa - Anopheles gambiae29Emilymozzie_genetrees_homologues_demo
Whole genome alignmentszebrafish
82Emilyzebrafish_alignments_demo




Questions and Answers

TopicVertebrates (or chordates)Non-vertebrates?UpdatedAdded byExercise/Answer
Species informationPanda
84EmilyPanda
Species informationZebrafish
84EmilyZebrafish
Species information
Metazoa (Mosquitoes)31EmilyMosquitos
Species information
Bacteria (Belliella baltica)31EmilyBelliela_baltica
Region in DetailHuman
84EmilyBRCA2_clones
Region in Detail - haplotypesHuman
84EmilyHaplotypes_patches
Gene - finding info about a geneHuman
84EmilyMYH9_gene
Gene - finding a gene by phenotypeHuman
84EmilyPAH_gene
Gene - finding info about a gene
Plants (Grape)31EmilyGrape_gene
BioMart - filter by protein domainMouse
84EmilyBioMart_domains
BioMart - convert IDsHuman
84EmilyBioMart_RefSeq
BioMart - find orthologues

Ciona intestinalis/Human 


84EmilyBioMart_orthologues
BioMart - find variantsHuman
84EmilyBioMart_SVs
BioMart - convert probes to genesHuman
84EmilyBioMart_probes
VariationHuman
84EmilyTAGAP_variant
VariationHuman
84EmilyMTHFR_variant
VariationHuman
75Emilystructural_variants.docx

Variation

Mouse
84Emilymouse_variant
Variation BioMartHuman
84EmilyBioMart_variation
VEPHuman
84EmilyCFTR_VEP
Compara - orthologuesHuman
84EmilyBRAF_compara
Compara - multiple alignmentsZebrafish
84Emilysardh_compara
Compara - syntenyHuman
84EmilyRHO_compara
Compara - pairwise alignmentsHuman
84EmilyBRCA2_compara
Paralogues BioMart comparaHuman
84Emilycompara_paralogues
RegulationHuman
84EmilySTX7_regulation
RegulationHuman
84EmilyHLA_regulation
Regulation BioMartHuman
84Emilyregulation_biomart
Advanced, multisectionHuman
84EmilyPDHA2_advanced
Advanced: VEP, variation mart, REST APIHuman
89VictoriaWrap-up exercise
VEP - HGVS notationHuman
76EmilyHGVS_VEP.docx
VEP - SVsHuman
76EmilySV_VEP.docx
VEP - VCF filesHuman
76EmilyVCF_VEP.docx test_chr21.vcf
Regulation - using new build track hubHuman
75 (with hub)EmilySTX7_regulation_update.docx
Regulation - using new build track hubHuman
75 (with hub)EmilyHLA_regulation_update.docx
Region in Detail
Plants (Arabidopsis)22EmilyMIR395_region.docx
Region in Detail
Plants (Grape)22EmilyMADS4_region.docx
Gene
Plants (Potato)22EmilyASC-1_gene.docx
BioMart - domains
Plants (Potato and maize)31Emilybiomart_plant_domains
BioMart - ID conversion
Plants (Arabidopsis)22EmilyUniprot_BioMart.docx
BioMart - probes
Plants (Arabidopsis)22Emilyprobes_BioMart.docx
RegionMouse
75EmilyUsh1c_region.docx
GeneMouse
75EmilyChd7_gene.docx
RegionMouse
75EmilyCLU_region.docx
Gene + RegionMouse
75EmilyPVRL2_gene.docx
Gene + RegionMouse
75EmilyZfp746_gene.docx
GeneMouse
75EmilyDpp6_gene.docx
BioMart - Gene - obesityHuman
71DeniseBioMart_Genes_obesity.docx
BioMart - Variation - rs IDsHuman
71DeniseBioMart_Variation_rsIDs.docx
BioMart - Gene - Domains & HomologsZebrafish and Human
71DeniseBioMart_Gene_domains_homologs.docx
Location tab - Lactase persistence (LCT, MCM6)Human
68DeniseLocationTab_Lactase.pptx
Variation - NPC1 geneHuman
73DeniseVariation_NPC1_human.docx
Variation - VEP - positions associated with lung cancerHuman
73DeniseVariation_VEP_lung_cancer.docx
Genomic location - Avian - RTN4 genelivestock, bird - turkey
75DeniseLocationTab_Avian.docx
Species page - Avianlivestock, bird - chicken
75DeniseSpecies_Page_Avian.docx
CCDC59 gene information - Avianbird - Zebrafinch
75DeniseGeneTab_Avian.docx
VEGFA gene tree and homologsHuman
75DeniseGene_tree_VEGFA.docx
DBH genomic alignment - Avianbird - Zebrafinch
75DeniseGenomic_alignments_DBH.docx
Variation - VEP - Avianlivestock, bird - turkey
75DeniseVariation_VEP_Avian.docx
Variation - Phenotype - Rose comblivestock, bird - chicken
83Emilychicken_rosecomb
BioMart - Affy Probes - Avianlivestock, bird - chicken
75DeniseBioMart_Avian_probes.docx
BioMart - FASTA seq chr 20- Avianlivestock, bird - chicken
75DeniseBioMart_Avian_export_fasta.docx
Assembly, orthologues, protein domainslivestock, bird - chicken
76DeniseIntro_chicken.docx
Synteny ATRXChicken and Human
75DeniseSynteny - Avian.docx
BRCA2 Alignment - Human - AvianHuman, chimp, birds
75DeniseGenomic_Alignment_BRCA2_human_avian.docx
Variation - VEP - bread wheat - VCF
Plants (bread wheat)22DeniseVEP_bread_wheat.docx
GTF - upload - bread wheat
Plants (bread wheat) 22DeniseGTF_upload_bread_wheat.docx
Genomic location bread wheat
Plants ( bread wheat) 22DeniseGenomic_location_bread_wheat.docx
BioMart - FASTA - bread wheat
Plants ( bread wheat) 22DeniseBioMart_bread_wheat.docx
Browser stats, prediction, GO
Plants (bread wheat)25DeniseIntro_stats_GO_domains.docx
Browser orthologs
Plant (arabidopsis)25DeniseIntro_ATHDH_orthologs.docx
BioMart missense variants
Plant (tomato)30Emilytomato_variants_biomart
BioMart FASTA Entrez Gene ID only
Plant (bread wheat)31EmilyBioMart_FASTA_Entrez
Variation tab ATCDSP32
Plant (arabidopsis)25DeniseBioMart_missense_chr6.docx
Variants data track in Location tab
Plant (tomato)30Emilytomato_variants_location
Variation tab
Plant (bread wheat)31Emilywheat_missense
VEP Ensembl default format
Plant (bread wheat)25DeniseVEP_default_Ensembl_bread_wheat.docx
Whole genomic alignment + synteny
Plant (arabidopsis)25Denisewhole_genome_alignments.docx
Gene trees + pan compara
Plant (arabidopsis)25Denisegene_tree_FUM1.docx
Homoeologues + polyploid view
Plant (bread wheat&barley)25Denisegene_tree_FUM1.docx
REST-API (several endpoints)human

DeniseREST_API_human.docx
Three browser RNASeq exerciseshuman

DeniseRNASeq_exercises.docx
Variation SNPs population geneticshuman
75DeniseVariation_rsIDs_human.docx
Variation CNVs FTO genehuman
75DeniseVariation_CNVs.docx
Genes - E. coli operon
Bacteria (E. coli)21EmilyEcoli_operon.docx
Pan-compara - bacteriahumanBacteria (Staph. aureus)21/74EmilyPan_compara_bacteria.docx
Fungal gene + region
Fungi (S. cerevisiae)19 or 20Emilyfungus_gene.docx
Genome, protein domains, GO
Metazoa (Mosquito)22GiuliettaMosquito_genome_proteindomains_GO.docx
BioMart + Browser
Protists (Leishmania)22Giuliettaleishmania_biomart_browser.docx
Assembly, genome stats, Location tab
Protists (Plasmodium vivax)22Deniseassembly_vivax.docx
number of Corynebacterium genomes, Location tab, Gene families
Bacteria (Corynebacterium sp)22DeniseCorynebacterium_sp.docx
BioMart, protein domains, FASTA export
Metazoa (Schistosoma mansoni)22DeniseSchistosoma_TM_domain.docx
BioMart, mtDNA, variants, XLS export
Fungi (S. cerevisiae)22Denisecerevisiae_variants_mtDNA.docx
number of fungi with variation data & details on Fusarium
Fungi (F. oxysporum)31EmilyFusarium_variation
Gene names and variation data in Plasmodium
Protists (P. falciparum)22DenisePlasmodium_variation.docx
Gene trees, homologs, sup45 gene in yeast
Fungi (S. cerevisiae)

22

DeniseFungi_homologs.docx
Synteny fruitfly et al
Metazoa (D. melanogaster)22Denisefruitfly_synteny.docx
Upload BED file for human APChuman
75Deniseupload_human_APC.docx
Upload gene features on the mouse karyotypemouse
75Deniseupload_mouse_karyotype.docx
Upload BAM file human chr 20human
75Deniseupload_BAM_human.docx
Finding a genome and its gene stats
Bacteria (Belliella baltica)22Denisegene_stats.docx
Exploring location tab of proV
Bacteria (E. coli)22DeniseLocation_tab_proV.docx
Exploring gene tab of era
Bacteria (E. coli)22DeniseGene_tab_era.docx
Finding a gene using sequence search
Bacteria (Sulolobus sp)22Denisesequence_search.docx
Exploring Comparative Genomics and GO terms
Bacteria (Staphylococcus aureus)22DeniseOrthologous_and_GO.docx
Upload BigWig bacteria
Bacteria (E. coli)22DeniseUpload_big_wig.docx
Variation - VEP - indel
Bacteria (Bacteroides fragilis)22DeniseVEP_indel_bacteria.docx
Variants and resequencing datalivestock - sheep and mouse
76DeniseIntro_sheep.docx






Browsing GRCh38 (bite sized exercises)human
76DeniseBite_sized_GRCh38.docx
Gene and transcripts (basic, phenotype, GO terms, UniProt)human
76Giuliettahuman_myh9
Gene and transcript (orthologue, protein summary)mouse
76Giuliettamouse_dpp6
Region in Detail (RNASeq, sequence variants)mouse and human
76Giuliettamouse_location_chr4
Species info, Arabidopis
Plants - arabodopsis31EmilyArabidopsis_info
Species info, Wheat
Plants - wheat31Emilywheat_info
Species info on INSDC annotated species
Fungi - Fusarium31Emilyfusarium_info
Species info on rice
Plants - rice31Emilyrice_info
Region in detail with polyploid view
Plants - wheat31Emilyregion_wheat_scaffold
Region in detail view adding array tracks
Plants - rice31Emilyrice_region
Gene
Plants - wheat31Emilywheat_PSBO
Gene
Metazoa - drosophila31EmilyDrosophila_ZAP3
Gene
Plants - wheat31Emilywheat_uba2
BioMart orthologues
Plants - wheat and barley31Emilybiomart_homologues_plants
BioMart with PHIBase filters
Fungi - Fusarium graminearum 31EmilyBiomart_phibase
BioMart ID conversion
Plants - wheat31Emilybiomart_plant_refseq
VEP with a VCF file
Plants - rice31Emilyrice_vep_vcf
Orthologues in fungi and pan compara
Fungi - S. pombe31Emilypombe_orthologues
Barley whole genome alignments
Plants - Barley31Emilybarley_alignments
Species info by genus
Plants - solanum30EmilySolanum_species_info
Tomato gene
Plants - tomato30Emilytomato_gene
Gene trees and homologues in maize
plants - maize30Emilymaize_genetrees
species info, sheeplivestock - sheep
83Emilysheep_info

species info, cow

livestock - cow
83Emilycow_info
species info, chickenlivestock, bird - chicken
83Emilychicken_info
species info, piglivestock - pig
83Emilypig_info
Cow region in detaillivestock - cow
83EmilyCow_region
sheep regionlivestock - sheep
83EmilySheep_region
chicken genelivestock, bird - chicken
83Emilychicken_myh9
finding a gene with a phenotypelivestock - pig
83Emilypig_phenotype
cow genelivestock - cow
83Emilycow_NIPBL
biomart filter by region and domainlivestock, bird - chicken
83Emilychicken_domains_biomart
biomart orthologueslivestock - cow, chicken
83Emilybiomart_cow_orthologues
biomart convert IDslivestock - pig
83Emilybiomart_pig_refseq
biomart variationlivestock - cow
83Emilycow_SVs_biomart
biomart array probeslivestock, bird - chicken
83Emilychicken_probes_biomart
pig variationlivestock - pig
83Emilypig_variant
chicken missense snplivestock, bird - chicken
83Emilychicken_snp
braf orthologueslivestock, bird - chicken
83Emilychicken_braf
sardh orthologueslivestock - cow
83Emilycow_sardh
rho syntenyLivestock - sheep and pig
83Emilyrho_sheep
brca2 alignmentslivestock - cow
83Emilybrca2_cow
Cow VEP query with a VCF filelivestock - cow
83Emilycow_vcf_vep
Species infofish - cod
84Emilycod_info
Species info
metazoa - Ixodes scapularis 29Emilytick_info
region in detailzebrafish
82Emilyzebrafish_region
region in detail
metazoa - Anopheles gambiae29Emilymosquito_region
Gene informationzebrafish
82Emilyzebrafish_vegfaa
Gene information
metazoa - Anopheles gambiae29Emilymozzie_para
RNASeq gene expressionzebrafish
82Emilycdk1_rnaseq
BioMart genes by domain
metazoa - Tetranychus urticae 29Emilymite_domains_biomart
BioMart homologuesfish - stickleback and human
82Emilystickleback_orthologues
BioMart RefSeq IDszebrafish
82Emilyzebrafish_refseq
BioMart SVszebrafish
82Emilyzebrafish_SVs_biomart
BioMart array probeszebrafish
82Emilyzebrafish_probes_biomart
Exploring a SNPzebrafish
82Emilyzebrafish_snp
Exploring a SNP
metazoa - Anopheles gambiae29Emilymozzie_snp
Finding variants by a genezebrafish
82Emilytbx16_variants
VEP coordinateszebrafish
82Emilyatp5o_vep
compara orthologues
metazoa - Anopheles gambiae29Emilyscrb9_orthologues
compara synteny
metazoa - Anopheles gambiae and Drosophila melanogaster29Emilyfly_mozzie_synteny
compara whole genome aligmentszebrafish
82Emilyfish_brca_alignments
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