Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition
Scripts for the analysis presented in the article: Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition
Fastq files used for this analysis are available from GEO series GSE235181.
TT-seq and mNET-seq reads were aligned using STAR. ChIP-seq and ChIP-nexus reads were aligned using Bowtie2.
Annotation: The major isoform annotation used in the study is available in data/
Other scripts and routines for performing the analysis are available in data/GatheringRoutines and data/Utility, which can be obtained by sourcing the script data/setup.R.
If not sourced in the previous step, source the script data/processing_functions.R.
The analysis.R script provides step-by-step code to perform all of the analyses described in the article. The script generates all the necessary datasets to derive the conclusions of the study.
- Define the necessary information about the location of the input BAM files, the location of the output directory, etc.
- Create RLE tracks for each datasets used in the study.
- Run the routines for read counting on the different datasets.
- Perform differential expression analysis to identify genes with significant changes in RNA synthesis (based on TT-seq data).
- Calculate the promoter-proximal occupancy of RNA polymerase (Pol) II from mNET-seq data (incl. routines for determining pause positions and defining promoter-proximal regions).
- Classification of genes based on expression pattern and gene clustering based on transcription kinetic parameters.
- Exponential fitting of ChIP-nexus data (following a time course of transcription initiation inhibition).
- Estimation of productive initiation frequency, apparent pause duration, promoter-proximal Pol II half-life, total turnover rate and termination fraction.
- rtracklayer 1.58.0
- GenomicAlignments 1.34.0
- Rsamtools 2.14.0
- dplyr 1.0.9
- doParallel 1.0.17
- DESeq2 1.38.0