Classes 7 13 - mestato/EPP622_2024 GitHub Wiki
Class 7. Tuesday September 10 - Loops, Read QC and trimming
- In person and recorded.
- Slides
- For Loop Anatomy
- Lab - For Loops
- Suggested Reading/Viewing
- Stoler and Nekrutenko 2021 Sequencing error profiles of Illumina sequencing instruments
- Video Intro to Sequencing by Synthesis - From Illumina
- Class 7 Recording
Class 8. Thursday September 12 - For loops and Quality check
- In person and recorded.
- Slides - Read Mapping and secure copy
- Video of lecture - Because we are a bit behind on the labs, we'll do lab only in class. Please plan to review the slides and watch the lecture.
- Lab - For Loops continued
- Lab - Read QC and trimming
- Video of lab
Class 9. Tuesday September 17 - Read trimming and mapping
- In person and recorded.
- Slides - Read Mapping and secure copy
- Video of lecture - We will be going through trimming and read mapping labs in this class so not a bad idea to go through this lecture video if you haven't already
- Lab - Read QC and trimming continued
- Lab - Read mapping
- Class Recording
Class 10. Thursday September 19 - Variant calling
- In person and recorded.
- Slides on Project Organization
- Slides on Variant Calling
- Lab - Variant Calling
- Reading
- Old but a good overview - A beginners guide to SNP calling from high-throughput DNA-sequencing data Altmann et al 2012
- Deep Variant may be a better option than GATK - Comparison of GATK and DeepVariant by trio sequencing Lin et al 2022
- More on the GATK pipeline we are using
- Class Recording
Class 11. Tuesday September 24 - Variant impact
- In person and recorded
- Slides on Data Management
- Slides on GBS and vcf file format
- Github Markdown Resources for Test #2
- How to use Github Wiki - Recording
- Markdown Cheatsheet
- Class Recording
- The above recording has poor sound quality for the lab. Please try to work thorugh the wiki directly or consider going through the similar (but not identical!) lab recording from 2022