1/ Do you have a list of @ensembl IDs that you want to convert to IDs from other databases?

Here's how you can retrieve the @NCBI gene IDs from a list of #Ensembl IDs. A thread...🧵

#genomics #bioinformatics #tweetorial #Ensembltraining 🧬 2/ The #BioMart tool is what you’re going to need for this task. You can find it in the blue header from the @ensembl homepage: ensembl.org/biomart/martvi…

1/ From ~20,000 coding genes in humans, biological complexity is also the result of gene/transcript expression levels in different tissues 📈

Want to see the expression of a #gene using @ensembl? A thread...🧵

#genomics #bioinformatics #tweetorial #Ensembltraining 🧬 2/ Gene-level tissue-specific expression patterns from @ExpressionAtlas are displayed in the Gene tab. Just search for your gene of interest, click through to the gene tab and then click on ‘Gene Expression’ in the left-hand menu. Let’s use SERPINA3 as an example:

1/ Do you want to know if a variant will affect the structure and function of a protein?

We’ve got lots of tools and #data in @ensembl to help you investigate and we’re here to show you how! A thread...🧵

#genomics #bioinformatics # #tweetorial #Ensembltraining🧬 2/ If you are working with human 🧑‍🤝‍🧑 variation data, genome-wide variant deleteriousness rankings from the CADD algorithm are available as well as pathogenicity predictions from SIFT, Polyphen-2, REVEL, MutationAssessor and MetaLR for missense variants.

1/ My favourite gene has 15 transcripts, which one should I use for further analysis? To report the position of variants? To design primers for? 🤯

This #tweetorial will show you how to filter and prioritise transcripts… 🧵

#genomics #bioinformatics #Ensembltraining 🧬 2/ To start, look for the #canonical tag in the flags column of the transcript table. The canonical transcript is based on conservation, expression, concordance with @appris_cnio and @uniprot, length, clinically important variants and completeness.

1/ Are you ready for 🎄🎅Chirstmas #Tweetorial? Whether you need the sequence for a single exon or whole #genome we got you covered! In the spirit of #Christmas, we will use Vitis vinifera 🍇 🍷in our example
#genomics #bioinformatics #Ensembltraining 2/ If you need the sequence of a single #gene, you can search for the gene symbol or ID from Ensembl homepage and click on ‘Sequence’ in the menu on the left

1/
It’s another Thursday, and that means it’s time for another #tweetorial! Today, we want to show you how you can view RefSeq #annotations on Ensembl 🥳

#bioinf #genomics #assembly #EnsemblTraining 2/
While Ensembl gene models are annotated directly on the reference genome, #RefSeq are annotated on mRNA sequences. In other words: genome browsers will have different annotation methods, so you might be interested in comparing these annotations side-by-side 📖🤔

1/ You’ve sequenced your samples and identified variants. Great! 🙌

Now, here's how you can use @ensembl to find out the effect of your variants on #protein structures and interactions. A thread...🧵

#genomics #bioinformatics #tweetorial #Ensembltraining 🧬 2/ The Variant Effect Predictor (VEP) is what you’re going to need for this task. You can find it in the blue header from the @ensembl homepage: ensembl.org/info/docs/tool…

#VEP

1/ Do you need reference sequence files from #Ensembl? All of the different files available can be confusing. Here’s a thread to help you decide which files you need…🧵

#genomics #bioinformatics #tweetorial #Ensembltraining🧬 2/ Whole-genome reference files for each species in Ensembl can be found on the FTP site 🧑‍🤝‍🧑🐭🐄🐶🐟

👉 ftp.ensembl.org

If you’re studying non-vertebrate species, you’ll need to use the Ensembl Genomes FTP site 🌾🦠🦟

👉 ftp.ensemblgenomes.org

1/ Knowing the frequency for alleles of genomic variants in populations around the world helps us understand phenotypes and disease 🌎🌍🌏

We’re here to take you through the data in @ensembl step-by-step. A thread…🧵

#genomics #bioinformatics #tweetorial #Ensembltraining🧬 2/ The way you approach this problem will depend on if you are starting with a #gene of interest or if you already have the ID (e.g rs699) of a variant for which you want to find the observed allele frequencies.

Want to learn about a gene function, but there’s no functional data in your species of interest? Or maybe looking for a homologue of your fav gene in a model organism to carry out functional work? Look no further! This #tweetorial will show you how to find orthologues in @ensembl 2/14
Let’s start on the Ensembl homepage and search for our #gene of interest SCP2 by typing its name into the search box. Then go to the gene tab by clicking on the gene name in the search results.

#Ensembltraining #genomics #bioinformatics #EnsemblCompara