Files found in this directory:
- Part 1:
- Presentation on analyzing ChIP-seq data here
- 00_workshop_code.sh: Code used in the workshop for analyzing ChIP-seq data.
- 01_analyzing_chipseq_data.Rmd and 01_analyzing_chipseq_data_solution.html: Notes on ChIP-seq data analysis with links to additional resources.
- scripts/: Scripts I used to download an process all H3K27ac ChIP-seq data.
- Part 2:
- 00_cheatsheet_GRanges.Rmd: Reference card with GenomicRanges functions and methods.
- 02_introduction_r_rstudio.Rmd and 02_introduction_r_rstudio_solution.html: Notes on R analysis of ChIP-seq data
- Part 1
- Downloading a dataset from GEO.
- FASTQ quality control.
- Alignment.
- Post-processing.
- Peak calling.
- Visualization with IGV.
- Part 2
- Introduction to R and RStudio.
- Dealing with
GenomicRanges. - Differential ChIP-seq analysis with DESeq2.
GEO Dataset: GSE112221. PMID: 30136421
Samples SRAs:
| Sample names | Experiment ID |
|---|---|
| NL1_h3k27ac_h3k27ac_chipseq | SRR6880492 |
| Cirr1_h3k27ac_chipseq | SRR6880493 |
| HCC1_h3k27ac_chipseq | SRR6880494 |
| Cirr3_h3k27ac_chipseq | SRR6880495 |
| HCC3_h3k27ac_chipseq | SRR6880496 |
| NL1_input_chipseq | SRR6880507, SRR6880508 |
| Cirr1_input_chipseq | SRR6880509, SRR6880510 |
| HCC1_input_chipseq | SRR6880511, SRR6880512 |
| Cirr3_input_chipseq | SRR6880513, SRR6880514 |
| HCC3_input_chipseq | SRR6880515, SRR6880516 |