... | ... | @@ -44,28 +44,32 @@ BiocManager::install(c("ChIPseeker", "GenomicRanges", "rtracklayer", "TxDb.Hsapi |
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* Alignment ([Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml))
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* File formats ([fasta](https://en.wikipedia.org/wiki/FASTA_format), [fastq](https://en.wikipedia.org/wiki/FASTQ_format), [bam](https://en.wikipedia.org/wiki/SAM_(file_format)))
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* 16:30 [Data processing II](https://ascgitlab.helmholtz-muenchen.de/chromatin_summer_school_2022/workshops/data_processing_2)
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### Thursday
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* 9:00 [Data processing II](https://ascgitlab.helmholtz-muenchen.de/chromatin_summer_school_2022/workshops/data_processing_2)
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* Genome coverage ([Deeptools](https://deeptools.readthedocs.io/en/develop/))
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* Peak finding ([MACS2](https://github.com/macs3-project/MACS))
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* File formats ([bed](https://en.wikipedia.org/wiki/BED_(file_format)), [bedgraph](https://genome.ucsc.edu/goldenpath/help/bedgraph.html))
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* IGV session
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### Thursday
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* 9:00 [Basic Dataviz with Deeptools](https://ascgitlab.helmholtz-muenchen.de/chromatin_summer_school_2022/workshops/dataviz_deeptools)
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* 10:30 [Basic Dataviz with Deeptools](https://ascgitlab.helmholtz-muenchen.de/chromatin_summer_school_2022/workshops/dataviz_deeptools)
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* profile plot
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* heatmap
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* 10:00 [Motif Search](https://ascgitlab.helmholtz-muenchen.de/chromatin_summer_school_2022/workshops/motif_search)
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* consensus peaks with [bedtools](https://bedtools.readthedocs.io/en/latest/)
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* find motifs with [Homer](http://homer.ucsd.edu/homer/motif/index.html)
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* 11:00 Snakemake final exercise
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* [implement Deeptools profile plot in Snakemake](https://ascgitlab.helmholtz-muenchen.de/chromatin_summer_school_2022/wiki/-/wikis/Snakemake-Final-Exercise)
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* 12:00 Interpretation of workflow results
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* IGV session
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* Bonus
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* [Motif Search](https://ascgitlab.helmholtz-muenchen.de/chromatin_summer_school_2022/workshops/motif_search)
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* consensus peaks with [bedtools](https://bedtools.readthedocs.io/en/latest/)
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* find motifs with [Homer](http://homer.ucsd.edu/homer/motif/index.html)
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* Snakemake final exercise
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* [implement Deeptools profile plot in Snakemake](https://ascgitlab.helmholtz-muenchen.de/chromatin_summer_school_2022/wiki/-/wikis/Snakemake-Final-Exercise)
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* 13:00 Lunch
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* 14:00 External seminar
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... | ... | |