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      mRNA-Seq Workshop

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Introduction and Lectures
Intro to the Workshop and Core
Schedule
What is Bioinformatics/Genomics?
Experimental Design and Cost Estimation
RNA Sequencing Technologies - Dr. Lutz Froenicke
Support
Using Zoom
Using Slack
Cheat Sheets
Software and Links
Scripts
Prerequisites
CLI - Logging in and Transferring Files
CLI - Intro to Command-Line
CLI - Advanced Command-Line (extra)
CLI - Running jobs on the Cluster and using modules
R - Getting Started
R - Intro to R
R - Prepare Data in R (extra)
R - Data in R (extra)
More Materials (extra)
Data Reduction
Files and Filetypes
Prepare dataset
Preprocessing raw data
Indexing a Genome
Alignment with Star
Generating counts tables
Alignment/Counts with Salmon (Extra)
Data analysis
Prepare R for data analysis
Annotation from BioMart
Differential Expression Analysis
Pathway Analysis
Comparison between STAR and Salmon
ETC
Closing thoughts
Workshop Photos
Github page
Report Errors
Biocore website

Retreiving Annotation via biomart

Annotation from BioMart with Ensembl names is most flexible way to retrieve tabular annotation for an organism.

  1. The Biomart start page should look like …

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  1. First select the dataset, for gene expression experiment select Ensembl Genes 100 (version 100). The current version as of this workshop.

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  1. Then the Organism, Here Mouse genes which is based on the GRCm38.p6 genome.

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  1. You can choose to filter to only a subset of genes. Or a chromosome, or regions. We won’t filter here. BY default, all genes in the genome are selected.

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  1. Next select the attributes you want in the table.

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  1. Expand the ‘GENE’ tab, and select the attributes you want to retreive. HERE recreate the list you see on the left side.

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  1. Click “Results” (Top left -ish).

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  1. Select “GO”, to download a tab-separated value (tsv) file.

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  1. The file will save as “mart_export.txt”, put the file into our working directory, rename to “ensembl_mm_100.tsv” and open the file in Excel to view the annotation.