Genomake (genomic make) is a python package to analyze genomic data.
This package is a WIP.
Check the documentation to get started.
Chromake is a snakemake pipeline to analyze ATAC-seq and ChIP-seq sequencing experiment.
It will supports peak calling for the epigenetic marks H3K27Ac, H3K27me3, and H2Aub (H2A Ubiquitination) and for ATAC-seq experiment:
| Experiment | Epigenetic mark | Full name | Config recognized names |
|---|---|---|---|
| ChIP-seq | H3K27Ac | Acetylation of the lysine residue at N-terminal position 27 of the histone H3 protein | H3K27AC |
| ChIP-seq | H3K27me3 | Tri-methylation of lysine 27 on histone H3 protein | H3K27ME3 |
| ChIP-seq | H2Aub | Histone 2A Ubiquitination | H2AUB |
| ATAC-seq | None | Assay for Transposase-Accessible Chromatin | ATAC |
Steps realized:
1. FASTQ trimming using cutadapt
2. QC (fastqc and multiqc) of raw and trimmed fastq files.
3. Alignment on genome (using bowtie2).
4. Peak calling (using macs2).
5. Read count (macs3) /!\ WIP /!\
6. Preliminary analysis and report generation (quarto report with PCA, heatmap, and some standard QC) /!\ Not a priority. /!\