TT-seq synthesis rate reproduction (SpikeinMedian)

This repository reproduces synthesis rate calculations from TT-seq and RNA-seq data from Erdogdu et al. (2026), using spike-in normalization. You can download the structured code and the input files and follow the instructions below to calculate RNA synthesis rates: - The required RData inputs for each experiment must be placed in: data/BRD234_inhibition - Each directory should contain: bam.files.RData bam.files.mat.RData database.merge.htseq.RPKs.antisense.corrected.RData alternative.sequencing.depth.RData alternative.cross.contamination.RData How to run Snakemake manually in a conda environment 1. Create and activate an environment with Snakemake: conda create -n ttseq_synth -c conda-forge -c bioconda snakemake conda activate ttseq_synth 2. Download this repository and navigate to Erdogdu_2026_synthesis_rate/TTseq_synthesis_rates: cd Erdogdu_2026_synthesis_rate/TTseq_synthesis_rates 3. Run the workflow snakemake -j 2Running this pipeline will create: Erdogdu_2026_synthesis_rate/results/BRD234_inhibition/total.synthesis.rates.replicate.list.SpikeinMedian.RData