Child pages
  • Ensembl exercises
Skip to end of metadata
Go to start of metadata

human_myh9.docx

This page contains links to all the exercises the Outreach team have available. You can use these to construct coursebooks for specific courses. The latest update is shown for each exercise, so if it's not the current release, you might want to check it (and its answers) against the website. If you do update an exercise, please re-post your new exercise and solution (or send it to someone from Outreach to do it).

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
BioMart walkthrough - human genesHuman 76Emilywalk_through_biomart_e76.docx
Browser walkthrough sir2 gene Fungi (yeast)22Denisewalkthrough_yeast.docx
Browser walkthrough DREB gene Plants (bread wheat)22Denisewalkthrough_wheat.docx
Finding species dataMultiAll76/23EmilySpecies_data.docx
Region in detail viewHuman 75EmilyRegion_in_detail_walkthrough.docx
Gene and transcript tabsHuman 75EmilyGene_transcript_tabs_walkthrough.docx
Variation in the browserHuman 76Emilyvariation_in_the_browser_walkthrough.docx
VEP online tool with default formatHuman 76EmilyVEP_online_tool.docx
Compara in the browserHuman 76Emilycompara_walkthrough.docx
RegulationHuman 76Emilyregulation_walkthrough.docx
Upload BED file to view in EnsemblHuman 76EmilyBED_upload.docx
Attach BAM file to view in EnsemblHuman 76EmilyBAM_upload.docx
Perform a REST API queryHuman 75EmilyREST_query.docx
Browser, VEP and REST Bacteria22Denisebrowser_VEP_Rest.docx
General walkthrough with Variation slantHuman 75Emilyvariation_browser.docx
BioMart with variation slantHuman 75Emilyvariation_biomart.docx


Questions and Answers

TopicVertebrates (or chordates)Non-vertebrates?UpdatedAdded byExercise/Answer
Species informationPanda 76EmilyPanda.docx
Species informationZebrafish 76EmilyZebrafish.docx
Species information Metazoa (Mosquitoes)23EmilyMosquitos.docx
Species information Bacteria (Belliella baltica)23EmilyBelliela_baltica.docx
Region in DetailHuman 76EmilyBRCA2_clones.docx
Region in Detail - haplotypesHuman 76EmilyHaplotypes_patches.docx
Gene - finding info about a geneHuman 76EmilyMYH9_gene.docx
Gene - finding a gene by phenotypeHuman 76EmilyPAH_gene.docx
Gene - finding info about a gene Plants (Grape)22EmilyGrape_gene.docx
BioMart - filter by protein domainMouse 76EmilyBioMart_domains.docx
BioMart - convert IDsHuman 76EmilyBioMart_RefSeq.docx
BioMart - find orthologues

Ciona intestinalis/Human 

 76EmilyBioMart_orthologues.docx
BioMart - find variantsHuman 76EmilyBioMart_SVs.docx
BioMart - convert probes to genesHuman 76EmilyBioMart_probes.docx
VariationHuman 76EmilyTAGAP_variant.docx
VariationHuman 75EmilyMTHFR_variant.docx
VariationHuman 75Emilystructural_variants.docx

Variation

Mouse 76Emilymouse_variant.docx
VEPHuman 76EmilyCFTR_VEP.docx
Compara - orthologuesHuman 76EmilyBRAF_compara.docx
Compara - multiple alignmentsZebrafish 76Emilydbh_compara.docx
Compara - syntenyHuman 76EmilyRHO_compara.docx
Compara - pairwise alignmentsHuman 76EmilyBRCA2_compara.docx
RegulationHuman 76EmilySTX7_regulation.docx
RegulationHuman 76EmilyHLA_regulation.docx
Advanced, multisectionHuman 76EmilyPDHA2_advanced.docx
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)22Emilydomains_BioMart.docx
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 geneTurkey 75DeniseLocationTab_Avian.docx
Species page - AvianChicken 75DeniseSpecies_Page_Avian.docx
CCDC59 gene information - AvianZebrafinch 75DeniseGeneTab_Avian.docx
VEGFA gene tree and homologsHuman 75DeniseGene_tree_VEGFA.docx
DBH genomic alignment - AvianZebrafinch 75DeniseGenomic_alignments_DBH.docx
Variation - VEP - AvianTurkey 75DeniseVariation_VEP_Avian.docx
Variation - Phenotype - Rose combChicken 75DeniseVariation_Avian_phenotype.docx
BioMart - Affy Probes - AvianChicken 75DeniseBioMart_Avian_probes.docx
BioMart - FASTA seq chr 20- AvianChicken 75DeniseBioMart_Avian_export_fasta.docx
Assembly, orthologues, protein domainsChicken 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
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)22DeniseFusarium_variation.docx
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 datasheep 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
  • No labels