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      RNA-Seq Analysis

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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
Zoom
Slack
Cheat Sheets
Software and Links
Scripts
Prerequisites
CLI
R
Cluster Computing
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
DE Quizzes R Code
Pathway Analysis
Enrichment Quizzes R Code
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 104 (version 104). The current version as of this workshop.

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  1. Then the Organism, Here Mouse genes which is based on the GRCm39 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 retrieve. 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_104.tsv” and open the file in Excel to view the annotation.