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Ensembl Exercises

This page contains links to all the exercises and walkthroughs the Ensembl 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, as they were made for a specific course and have not been updated since. Those labelled E are the Ensembl release and those labelled EG are the Ensembl Genomes release.

Our blog contains more information about how you can plan and teach your own Ensembl browser workshop, using these exercises.


Topic Species Updated Walkthrough
Basic browser walkthrough - ABCD1 gene Human E76 walk_through_browser_e76.docx
Basic browser walkthrough – OS01G0775500 gene Plants (rice) EG35 RiD_riceOS01G0775500.docx
BioMart walkthrough - human genes Human E84 Demo BioMart
Browser walkthrough sir2gene Fungi (yeast) EG22 walkthrough_yeast.docx
Browser walkthrough DREBgene Plants (bread wheat) EG22 walkthrough_wheat.docx
Browser walkthrough AP1gene Plants (Arabidopsis) EG25 walkthrough_arabidopsis.docx
Finding species data Multi E84/EG31 Species_data
Region in detail view Human E84 Region_in_detail_walkthrough
Region in detail view—SHH Human E84 Region_in_detail_SHH
Gene and transcript tabs Human E84 Gene_transcript_tabs_walkthrough
Gene and transcript tabs – OS01G0775500 gene Plants (rice) EG35 G&T_riceOS01G0775500.docx
Gene and transcript tabs — SHH Human E89 Genes and transcripts — SHH
Variation in the browser Human E84 variation_in_the_browser_walkthrough
Variation in the browser – OS01G0775500 gene Plants (rice) EG35 variation_riceOS01G0775500.docx
Variation in the browser – SHH Human E89 Variation—SHH
VEP online tool with default format Human E84 VEP_online_tool
Compara in the browser Human E84 compara_walkthrough
Regulation Human E84 regulation_walkthrough
Upload BED file to view in Ensembl Human E84 BED_upload
Attach BAM file to view in Ensembl Human E84 BAM_upload
Perform a REST API query Human E84 REST_query
Browser, VEP and REST Bacteria EG22 browser_VEP_Rest.docx
General walkthrough with Variation slant Human E75 variation_browser.docx
BioMart with variation slant Human E75 variation_biomart.docx
BioMart, variation: barley Plants (barley) EG35 BioMart_variationBarley.docx
Region in detail view Plants - wheat EG31 wheat_region
Gene and transcript tabs of a PHI-base annotated gene Fungi - Zymoseptoria tritici EG31 ZT_phibase_gene
BioMart query with a wheat region Plants - wheat EG31 wheat_biomart_demo
Variation in wheat plants - wheat EG31 wheat_variation_demo
VEP in wheat plants - wheat EG31 wheat_vep_demo
Whole genome alignments plants - rice EG31 rice_alignments_demo
Gene trees and homologues plants - wheat EG31 wheat_gene_trees_homologues
Uploading BED files Fungi - Zymoseptoria tritici EG31 fungi_bed
Attaching RNASeq files from the Track Hub Registry plants - rice EG31 Rice_RNAseq_trackhub
Gene and transcript tabs plants - barley EG30 Barley_gene_demo
BioMart rice region plants - rice EG30 rice_biomart_demo
Variation in rice plants - rice EG30 rice_variation_demo
Region in cow livestock - cow E83 cow_region_demo
Gene and transcript tabs livestock - pig E83 pig_gene_demo
BioMart sheep gene list livestock - sheep E83 sheep_biomart_demo
Variation livestock, bird - chicken E83 chicken_variation_demo
VEP with coordinates livestock - sheep E83 sheep_vep_demo
Compara gene trees and homologues livestock - cow E83 cow_genetrees_orthologues_demo
Compara alignments livestock - pig E83 pig_alignment_hoxD_demo
Region in detail metazoa - Anopheles gambiae EG29 Region_mozzies
Gene and transcript tabs zebrafish E82 zebrafish_gene_demo
BioMart gene list metazoa - Anopheles gambiae EG29 mozzie_biomart_demo
Variation in the browser zebrafish E82 zebrafish_variation_demo
VEP coordinates metazoa - Anopheles gambiae EG29 mozzie_VEP_demo
Gene trees and homologues metazoa - Anopheles gambiae EG29 mozzie_genetrees_homologues_demo
Whole genome alignments zebrafish E82 zebrafish_alignments_demo

Questions and Answers

This table contains questions and answers. In Ensembl-run workshops, we ask the participants to work through these by themselves, helping out where needed.

Topic Species Updated Walkthrough
Species information Panda E84 Panda
Species information Zebrafish E84 Zebrafish
Species information Metazoa (Mosquitoes) EG31 Mosquitos
Species information Bacteria (Belliella baltica) EG31 Belliela_baltica
Region in Detail Human E84 BRCA2_clones
Region in Detail - haplotypes Human E84 Haplotypes_patches
Gene - finding info about a gene Human E84 MYH9_gene
Gene - finding a gene by phenotype Human E84 PAH_gene
Gene - finding info about a gene Plants (Grape) EG31 Grape_gene
BioMart - filter by protein domain Mouse E84 BioMart_domains
BioMart - convert IDs Human E84 BioMart_RefSeq
BioMart - find orthologues Ciona intestinalis/Human E84 BioMart_orthologues
BioMart - find variants Human E84 BioMart_SVs
BioMart - convert probes to genes Human E84 BioMart_probes
Variation Human E84 TAGAP_variant
Variation Human E84 MTHFR_variant
Variation Human E75 structural_variants.docx
Variation Mouse E84 mouse_variant
Variation BioMart Human E84 BioMart_variation
Compara - orthologues Human E84 BRAF_compara
Compara - multiple alignments Zebrafish E84 sardh_compara
Compara - synteny Human E84 RHO_compara
Compara - pairwise alignments Human E84 BRCA2_compara
Paralogues BioMart compara Human E84 compara_paralogues
Regulation Human E84 STX7_regulation
Regulation Human E84 HLA_regulation
Regulation BioMart Human E84 regulation_biomart
Advanced, multisection Human E84 PDHA2_advanced
Advanced: VEP, variation mart, REST API Human E89 Wrap-up exercise
VEP - HGVS notation Human E76 HGVS_VEP.docx
VEP - SVs Human E76 SV_VEP.docx
VEP - VCF files Human E76 VCF_VEP.docx test_chr21.vcf
Region in Detail Plants (Arabidopsis) EG22 MIR395_region.docx
Region in Detail Plants (Grape) EG22 MADS4_region.docx
Gene Plants (Potato) EG22 ASC-1_gene.docx
BioMart - domains Plants (Potato and maize) EG31 biomart_plant_domains
BioMart - ID conversion Plants (Arabidopsis) EG22 Uniprot_BioMart.docx
BioMart - probes Plants (Arabidopsis) EG22 probes_BioMart.docx
Region Mouse E75 Ush1c_region.docx
Gene Mouse E75 Chd7_gene.docx
Region Mouse E75 CLU_region.docx
Gene + Region Mouse E75 PVRL2_gene.docx
Gene + Region Mouse E75 Zfp746_gene.docx
Gene Mouse E75 Dpp6_gene.docx
BioMart - Gene - obesity Human E71 BioMart_Genes_obesity.docx
BioMart - Variation - rs IDs Human E71 BioMart_Variation_rsIDs.docx
BioMart - Gene - Domains & Homologs Zebrafish and Human E71 BioMart_Gene_domains_homologs.docx
Location tab - Lactase persistence (LCT, MCM6) Human E68 LocationTab_Lactase.pptx
Variation - NPC1 gene Human E73 Variation_NPC1_human.docx
Variation - VEP - positions associated with lung cancer Human E73 Variation_VEP_lung_cancer.docx
Genomic location - Avian - RTN4 gene livestock, bird - turkey E75 LocationTab_Avian.docx
Species page - Avian livestock, bird - chicken E75 Species_Page_Avian.docx
CCDC59 gene information - Avian bird - Zebrafinch E75 GeneTab_Avian.docx
VEGFA gene tree and homologs Human E75 Gene_tree_VEGFA.docx
DBH genomic alignment - Avian bird - Zebrafinch E75 Genomic_alignments_DBH.docx
Variation - VEP - Avian livestock, bird - turkey E75 Variation_VEP_Avian.docx
Variation - Phenotype - Rose comb livestock, bird - chicken E83 chicken_rosecomb
BioMart - Affy Probes - Avian livestock, bird - chicken E75 BioMart_Avian_probes.docx
BioMart - FASTA seq chr 20- Avian livestock, bird - chicken E75 BioMart_Avian_export_fasta.docx
Assembly, orthologues, protein domains livestock, bird - chicken E76 Intro_chicken.docx
Synteny ATRX Chicken and Human E75 Synteny - Avian.docx
BRCA2 Alignment - Human - Avian Human, chimp, birds E75 Genomic_Alignment_BRCA2_human_avian.docx
Variation - VEP - bread wheat - VCF Plants (bread wheat) EG22 VEP_bread_wheat.docx
GTF - upload - bread wheat Plants (bread wheat) EG22 GTF_upload_bread_wheat.docx
Genomic location bread wheat Plants ( bread wheat) EG22 Genomic_location_bread_wheat.docx
BioMart - FASTA - bread wheat Plants ( bread wheat) EG22 BioMart_bread_wheat.docx
Browser stats, prediction, GO Plants (bread wheat) EG25 Intro_stats_GO_domains.docx
Browser orthologs Plant (arabidopsis) EG25 Intro_ATHDH_orthologs.docx
BioMart missense variants Plant (tomato) EG30 tomato_variants_biomart
BioMart FASTA Entrez Gene ID only Plant (bread wheat) EG31 BioMart_FASTA_Entrez
Variation tab ATCDSP32 Plant (arabidopsis) EG25 BioMart_missense_chr6.docx
Variants data track in Location tab Plant (tomato) EG30 tomato_variants_location
Variation tab Plant (bread wheat) EG31 wheat_missense
VEP Ensembl default format Plant (bread wheat) EG25 VEP_default_Ensembl_bread_wheat.docx
Whole genomic alignment + synteny Plant (arabidopsis) EG25 whole_genome_alignments.docx
Gene trees + pan compara Plant (arabidopsis) EG25 gene_tree_FUM1.docx
Homoeologues + polyploid view Plant (bread wheat&barley) EG25 gene_tree_FUM1.docx
REST-API (several endpoints) human REST_API_human.docx
Three browser RNASeq exercises human RNASeq_exercises.docx
Variation SNPs population genetics human E75 Variation_rsIDs_human.docx
Variation CNVs FTO gene human E75 Variation_CNVs.docx
Genes - E. coli operon Bacteria (E. coli) EG21 Ecoli_operon.docx
Pan-compara - bacteria human, Bacteria (Staph. aureus) EG21/E74 Pan_compara_bacteria.docx
Fungal gene + region Fungi (S. cerevisiae) EG19 or EG20 fungus_gene.docx
Genome, protein domains, GO Metazoa (Mosquito) EG22 Mosquito_genome_proteindomains_GO.docx
BioMart + Browser Protists (Leishmania) EG22 leishmania_biomart_browser.docx
Assembly, genome stats, Location tab Protists (Plasmodium vivax) EG22 assembly_vivax.docx
number of Corynebacterium genomes, Location tab, Gene families Bacteria (Corynebacterium sp) EG22 Corynebacterium_sp.docx
BioMart, protein domains, FASTA export Metazoa (Schistosoma mansoni) EG22 Schistosoma_TM_domain.docx
BioMart, mtDNA, variants, XLS export Fungi (S. cerevisiae) EG22 cerevisiae_variants_mtDNA.docx
number of fungi with variation data & details on Fusarium Fungi (F. oxysporum) EG31 Fusarium_variation
Gene names and variation data in Plasmodium Protists (P. falciparum) EG22 Plasmodium_variation.docx
Gene trees, homologs, sup45 gene in yeast Fungi (S. cerevisiae) EG22 Fungi_homologs.docx
Synteny fruitfly et al Metazoa (D. melanogaster) EG22 fruitfly_synteny.docx
Upload BED file for human APC human E75 upload_human_APC.docx
Upload gene features on the mouse karyotype mouse E75 upload_mouse_karyotype.docx
Upload BAM file human chr 20 human E75 upload_BAM_human.docx
Finding a genome and its gene stats Bacteria (Belliella baltica) EG22 gene_stats.docx
Exploring location tab of proV Bacteria (E. coli) EG22 Location_tab_proV.docx
Exploring gene tab of era Bacteria (E. coli) EG22 Gene_tab_era.docx
Finding a gene using sequence search Bacteria (Sulolobus sp) EG22 sequence_search.docx
Exploring Comparative Genomics and GO terms Bacteria (Staphylococcus aureus) EG22 Orthologous_and_GO.docx
Upload BigWig bacteria Bacteria (E. coli) EG22 Upload_big_wig.docx
Variation - VEP - indel Bacteria (Bacteroides fragilis) EG22 VEP_indel_bacteria.docx
Variants and resequencing data livestock - sheep and mouse E76 Intro_sheep.docx
Browsing GRCh38 (bite sized exercises) human E76 Bite_sized_GRCh38.docx
Gene and transcripts (basic, phenotype, GO terms, UniProt) human E76 human_myh9
Gene and transcript (orthologue, protein summary) mouse E76 mouse_dpp6
Region in Detail (RNASeq, sequence variants) mouse and human E76 mouse_location_chr4
Species info, Arabidopis Plants - arabodopsis EG31 Arabidopsis_info
Species info, Wheat Plants - wheat EG31 wheat_info
Species info on INSDC annotated species Fungi - Fusarium EG31 fusarium_info
Species info on rice Plants - rice EG31 rice_info
Region in detail with polyploid view Plants - wheat EG31 region_wheat_scaffold
Region in detail view adding array tracks Plants - rice EG31 rice_region
Gene Plants - wheat EG31 wheat_PSBO
Gene Metazoa - drosophila EG31 Drosophila_ZAP3
Gene Plants - wheat EG31 wheat_uba2
BioMart orthologues Plants - wheat and barley EG31 biomart_homologues_plants
BioMart with PHIBase filters Fungi - Fusarium graminearum EG31 Biomart_phibase
BioMart ID conversion Plants - wheat EG31 biomart_plant_refseq
VEP with a VCF file Plants - rice EG31 rice_vep_vcf
Orthologues in fungi and pan compara Fungi - S. pombe EG31 pombe_orthologues
Barley whole genome alignments Plants - Barley EG31 barley_alignments
Species info by genus Plants - solanum EG30 Solanum_species_info
Tomato gene Plants - tomato EG30 tomato_gene
Gene trees and homologues in maize plants - maize EG30 maize_genetrees
species info, sheep livestock - sheep E83 sheep_info
species info, cow livestock - cow E83 cow_info
species info, chicken livestock, bird - chicken E83 chicken_info
species info, pig livestock - pig E83 pig_info
Cow region in detail livestock - cow E83 Cow_region
sheep region livestock - sheep E83 Sheep_region
chicken gene livestock, bird - chicken E83 chicken_myh9
finding a gene with a phenotype livestock - pig E83 pig_phenotype
cow gene livestock - cow E83 cow_NIPBL
biomart filter by region and domain livestock, bird - chicken E83 chicken_domains_biomart
biomart orthologues livestock - cow, chicken E83 biomart_cow_orthologues
biomart convert IDs livestock - pig E83 biomart_pig_refseq
biomart variation livestock - cow E83 cow_SVs_biomart
biomart array probes livestock, bird - chicken E83 chicken_probes_biomart
pig variation livestock - pig E83 pig_variant
chicken missense snp livestock, bird - chicken E83 chicken_snp
braf orthologues livestock, bird - chicken E83 chicken_braf
sardh orthologues livestock - cow E83 cow_sardh
rho synteny Livestock - sheep and pig E83 rho_sheep
brca2 alignments livestock - cow E83 brca2_cow
Cow VEP query with a VCF file livestock - cow E83 cow_vcf_vep
Species info fish - cod E84 cod_info
Species info metazoa - Ixodes scapularis EG29 tick_info
region in detail zebrafish E82 zebrafish_region
region in detail metazoa - Anopheles gambiae EG29 mosquito_region
Gene information zebrafish E82 zebrafish_vegfaa
Gene information metazoa - Anopheles gambiae EG29 mozzie_para
RNASeq gene expression zebrafish E82 cdk1_rnaseq
BioMart genes by domain metazoa - Tetranychus urticae EG29 mite_domains_biomart
BioMart homologues fish - stickleback and human E82 stickleback_orthologues
BioMart RefSeq IDs zebrafish E82 zebrafish_refseq
BioMart SVs zebrafish E82 zebrafish_SVs_biomart
BioMart array probes zebrafish E82 zebrafish_probes_biomart
Exploring a SNP zebrafish E82 zebrafish_snp
Exploring a SNP metazoa - Anopheles gambiae EG29 mozzie_snp
Finding variants by a gene zebrafish E82 tbx16_variants
VEP coordinates zebrafish E82 atp5o_vep
compara orthologues metazoa - Anopheles gambiae EG29 scrb9_orthologues
compara synteny metazoa - Anopheles gambiae and Drosophila melanogaster EG29 fly_mozzie_synteny
compara whole genome aligments zebrafish E82 fish_brca_alignments