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| Main Authors: | , |
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| Format: | Recurso digital |
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Zenodo
2026
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| Online Access: | https://doi.org/10.5281/zenodo.18403045 |
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Table of Contents:
- <p>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:</p> <p> </p> <p dir="auto">- The required RData inputs for each experiment must be placed in:</p> <ul> <li>data/BRD234_inhibition</li> </ul> <p>- Each directory should contain:</p> <ul> <li>bam.files.RData</li> <li>bam.files.mat.RData</li> <li>database.merge.htseq.RPKs.antisense.corrected.RData</li> <li>alternative.sequencing.depth.RData</li> <li>alternative.cross.contamination.RData</li> </ul> <div dir="auto"> <h3> </h3> <h3>How to run Snakemake manually in a conda environment</h3> </div> <p>1. Create and activate an environment with Snakemake:</p> <div dir="auto"> <pre><code>conda create -n ttseq_synth -c conda-forge -c bioconda snakemake conda activate ttseq_synth</code></pre> </div> <p> </p> <p>2. Download this repository and navigate to Erdogdu_2026_synthesis_rate/TTseq_synthesis_rates:</p> <div dir="auto"> <pre><code> cd Erdogdu_2026_synthesis_rate/TTseq_synthesis_rates</code></pre> <div> </div> </div> <p>3. Run the workflow</p> <div dir="auto"> <pre><code>snakemake -j 2</code><br><br>Running this pipeline will create:<br><br></pre> <div dir="auto"> <p>Erdogdu_2026_synthesis_rate/results/BRD234_inhibition/total.synthesis.rates.replicate.list.SpikeinMedian.RData</p> </div> </div>