Schedule is subject to change (but not the exam dates)
| Day & Time | Date | Topic | Reference |
|---|---|---|---|
| Tue 1:10 - 5:00 | 31-Mar | JetStream; Markdown; Git; Intro Linux | Buffalo: p. 1 - 54 (Chapters 1-3); p. 67 - 97 (Chapter 5); 125 - 165 (Chapter 7) |
| Thur 1:10 - 5:00 | 2-Apr | For Loops; BLAST | Chapter 6 of Bioinformatics for Beginners |
| Fri 1:10 - 2:00 | 3-Apr | Discussion: Linux, Git, BLAST | |
| Tue 1:10 - 5:00 | 7-Apr | BLAST continued | |
| Thur 1:10 - 5:00 | 9-Apr | Analyze BLAST results in R (tidyverse) | R for data science Chapters 4, 5, 6, 10, 18, 27; Buffalo Chapter 8. |
| Fri 1:10 - 2:00 | 10-Apr | Discussion: For loops, BLAST, upSet plots | |
| Tue 1:10 - 5:00 | 14-Apr | Multiple Sequence Alignment and Tree Building | Chapter 9 of Bioinformatics for Beginners |
| Thur 1:10 - 5:00 | 16-Apr | R SNPS; ggplot | Buffalo: Cahpter 8; R for data science Chapters 3, 12 |
| Fri 1:10 - 2:00 | 17-Apr | Discussion: Tidyverse, trees, etc | |
| Tue 1:10 - 5:00 | 21-Apr | GWAS | Wikipedia GWAS GWAS Q & A GWAS protocol |
| Thur 1:10 - 5:00 | 23-Apr | Shiny | |
| Fri 1:10 - 2:00 | 24-Apr | Help with Shiny | |
| Tue 1:10 - 5:00 | 28-Apr | Genome Assembly | |
| Thur 1:10 - 5:00 | 30-Apr | Methylation Analysis | |
| Fri 1:10 - 2:00 | 1-May | In Class Midterm + Take Home Midterm Posted | |
| Tue 1:10 - 5:00 | 5-May | Work on take home midterm | |
| Thur 1:10 - 5:00 | 7-May | Assembly and Methylation continued Midterm Due @ 1:10 | |
| Fri 1:10 - 2:00 | 8-May | Discussion: Methylation, assembly | |
| Tue 1:10 - 5:00 | 12-May | Illumina Sequence Data: QC and mapping | Buffalo: p. 339 - 351 (Start of Chapter 10 to Indexed FASTA Files) Wikipedia FastQ U Mich SAM wiki |
| Thur 1:10 - 5:00 | 14-May | Illumina: SNPs and IGV | Buffalo p. 355 - 377 (Start of Chapter 11 to Pileups with samtools pileup) |
| Fri 1:10 - 2:00 | 15-May | Discussion: Illumina, etc | |
| Tue 1:10 - 5:00 | 19-May | Illumina: RNAseq | |
| Thur 1:10 - 5:00 | 21-May | Illumina: RNAseq | |
| Fri 1:10 - 2:00 | 22-May | Discussion: RNAseq, etc | |
| Tue 1:10 - 5:00 | 26-May | Motif discovery | |
| Thur 1:10 - 5:00 | 28-May | Clustering | |
| Fri 1:10 - 2:00 | 29-May | Discussion: Genetic Networks | |
| Tue 1:10 - 5:00 | 2-Jun | Networks | |
| Thur 1:10 - 5:00 | 4-Jun | Metagenomics | |
| Fri | 5-Jun | Final Take Home Exam available | |
| Tue 5:00 PM | 09-Jun | Final Take Home Exam Due 5PM | |
| Wed 3:30 PM | 10-Jun | In Class Final |