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Scripts and files for the annual Short Read Analysis Workshop

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# Short Read Workshop 2025

This github repository holds the scripts and files for the 2025 Short Read Analysis Workshop, a biological data science course created by the DnA Lab (Dowell and Allen) at the University of Colorado Boulder. This course will teach the basics of RNA-seq analysis using a super computer, the bash language, R, and common bioinformatics software packages. This course assumes you will use a super computer for analysis.

This course is a reverse classroom course, where lectures are posted as videos to be watched the night before class. Video links and other general course information are available [here](https://biodatasci.colorado.edu/shortread/sr2024/). Data files will be provided to you on the AWS supercomputer that we are using for the course, and will be stored afterward on the University of Colorado Fiji cluster for those who have access. All other materials and links are included in this repository.

Days 1-6 and day 10 of the workshop will be the same for all participants. Days 7-9 will be specific to the mini-project you've chosen:\
Project A - Single Cell RNA-seq (Canceled due to a lack of funding)
Project B - Multi-omics: RNA-seq/ChIP-seq/ATAC-seq

We hope you enjoy learning with us!

Please let us know what you thought of the workshop: [https://forms.gle/ZcCgC6yFT54YVvBG9](https://forms.gle/ZcCgC6yFT54YVvBG9)

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