The purpose of this repository is to provide the scripts that are used to produce the figures related to the analysis of ChIP-seq and RNA-seq datasets for the manuscript by Müthel, S. et al.
The ChIP-Seq sequencing data was processed using the PiGx-ChIPseq pipeline (version 0.0.16).
The resulting peak sets are in two different folders:
MACS peaks, contain peaks detected in each sample using MACS peak caller. IDR (irreproducible discovery rate) peaks contain peaks detected based on sample replicates.
The settings and sample sheet files used to run this pipeline can be found under ./data/chipseq.
See PiGx-ChIPseq documentation for more information: http://bioinformatics.mdc-berlin.de/pigx_docs/pigx-chip-seq.html#pigx-chip-seq
The RNA-seq data was processed using the PiGx-RNAseq pipeline (version 0.0.4).
We use the Salmon quantified gene-level raw read counts used for the analyses here.
The raw read counts along with settings and sample sheet files can be found under ./data/rnaseq/ folder.
See PiGx-RNAseq documentation for more information: http://bioinformatics.mdc-berlin.de/pigx_docs/pigx-rna-seq.html
This is a list of gene sets compiled either manually or using scripts. The metabolic genes from the KEGG Metabolic pathways for C.elegans was compiled using the script "get_kegg_genes.R".
./makeManuscriptFigures.Rmd : takes as input ChIPseq peaks and RNA-seq read counts and produces some figures and an html report.
To render the vignette type:
Rscript ./render.vignette.R
./results.2019.05.09 folder points to the results obtained at the time of the publication of the study.
The folder contains two HTML reports:
manuscript_analysis.htmlcontains the figures and tables as used for the manuscript using log2FoldChange threshold of 0.5 and FDR threshold of 0.05.manuscript_analysis.stricter_thresholds.htmlcontains the same analysis using stricter log2FoldChange (1) and FDR (0.001) thresholds.
Other folders starting with results followed by a date correspond to reanalysis of the same input on different dates because of for instance bug fixes due to package updates.
install.packages(c('ggplot2', 'ggfortify', 'VennDiagram', 'gprofiler2', 'UpSetR', 'DT', 'reshape2', 'data.table', 'scales', 'corrplot'))
BiocManager::install(c('RUVSeq', 'DESeq2', 'GenomicFeatures'))