Contents
- 1 Lecture 1: Introduction to High Throughput Sequencing Technology Lecture
- 2 Lecture 2: Command Line Basics (directories, head, wc, etc.)
- 3 Lecture 3: Command Line Basics (pipes, compression, and grep)
- 4 Lecture 4: Command Line Basics (find, cut, variables, scripting, and permissions)
- 5 Lecture 5: awk
- 6 Lecture 6: Logical operators, loops, and Xanadu (the UCHC computing server)
- 7 Lecture 7: Batch scripts, interactive sessions, and software installs
- 8 Lecture 8: Illumina data format, QC, and preprocessing
- 9 Lecture 9: fastx tools preprocessing
- 10 Lecture 10: Aligning Illumina data
- 11 Lecture 11: Transcription Factors Lecture
- 12 Lecture 12: Post-mapping processing with samtoola and bedtools
- 13 Lecture 13: The UCSC genome browser
- 14 Lecture 14: ChIP-seq peak calling
- 15 Lecture 15: Analyze ChIP-seq peaks with bedtools and awk
- 16 Lecture 16: de novo motif analysis
- 17 Lecture 17: Motif queries to genomes and databases
- 18 Lecture 18: Introduction to
R
- 19 Lecture 19: RNA-seq lecture
- 20 Lecture 20:
R functions and plotting
- 21 Lectures 21-23: RNA-seq in the command line
- 22 Lectures 24-25: RNA-seq in
R
- 23 Lectures 26-27: ATAC-seq
Thank you to everyone who took MEDS5420 in 2023. Also, A big thanks to Leighton Core, who shared his Functional Genomics class content with me. Dr. Core developed much of the basic command line utilities text and examples that were reproduced with his permission.