Class meetings are in Room 6117 Jordan Hall from 8:30 to 10:20 am on Mondays, Wednesdays, and Fridays
The Biostar Handbook is a resource for much of the reading
| Week | topics | Biostar Handbook Sections |
|---|---|---|
| 1 | Introduction to Linux and the command-line interface | 1, 2, 4 |
| 2 | Kinds of sequencing instruments | |
| 2 | experimental design | 8, 9, 10 |
| 2 | data preprocessing and quality control | |
| 3 | error correction and alignment | |
| 4 | Assembly - transcriptomes | |
| 4 | genomes | 22 |
| 5 | Re-sequencing & alignment | 17, 18, 23 |
| 6 | Discovery and genotyping of genetic variation | |
| 7 | R and R Studio - lectures and exercises through Software Carpentry website, sections 1 - 8 | |
| 8 | R and R Studio, continued - sections 9 - 12. Advanced: Data Carpentry for Genomics | |
| 9 | Transcriptome analysis: differential gene expression, annotation | 19, 20 |
| 10 | Genome analysis: ChIP-seq, DHS-seq, 3-D conformation | |
| 11 | Linux command-line tools: awk, sed, and bash | 15 |
| 12 | exploring parameter space - genome assembly, genetic variant analysis |
General advice on troubleshooting
Lior Pachter's list of sequencing-based assays: *Seq
The R statistical programming environment
OMICtools software database publication and website
Qiagen webpage of tutorials for CLC workbench programs
Colib'read project webpage on reference-assembly-free programs for SNP and indel detection and more