Simulated RNA-seq data

<p>Simulated RNA-seq data shows that histograms from p value sets with around one hundred&nbsp;&nbsp;true effects out of 20,000 features can be classified as &#39;uniform&#39;.&nbsp;RNA-seq data was simulated with polyester R package <a href="https://doi.org/10.1093/bioinformatics/btv272">(Frazee, 2015)</a> on 20,000 transcripts from human transcriptome&nbsp;using grid of 3, 6, and 10 replicates and 100, 200, 400, and 800 effects for two groups.&nbsp;Fold changes were set to 0.5 and 2.&nbsp;Differential expression was assessed using DESeq2 R package <a href="https://doi.org/10.1186/s13059-014-0550-8">(Love, 2014)</a> using default settings&nbsp;and group 1 versus group 2 contrast.&nbsp;Effects denotes in facet labels the number of true effects and N denotes number of replicates.&nbsp;Red line denotes QC threshold used for dividing p histograms into discrete classes.&nbsp;Workflow and code used to run this simulation is available on <a href="https://github.com/rstats-tartu/simulate-rnaseq">rstats-tartu/simulate-rnaseq</a>.</p> <p>&nbsp;</p> <p>Files</p> <ul> <li>de_simulation_results.csv -- merged and processed DE analysis results of simulated data.</li> <li>simulate-reads-2021-01-25.tar.gz -- raw DE analysis results&nbsp;on 20,000 transcripts from human transcriptome&nbsp;using grid of 3, 6, and 10 replicates and 100, 200, 400, and 800 effects for two groups.&nbsp;Fold changes were set to 0.5, 1, and 2.&nbsp;Differential expression was assessed using DESeq2 with default settings.</li> <li>simulate-rnaseq.tar.gz -- snakemake workflow and input fasta file&nbsp;to simulate RNA-seq data with polyester and analyse results with DESeq2. Adjust settings in config.yaml to customise simulation. Includes software to run workflow on Linux, given that <a href="https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh">Conda</a> and <a href="https://snakemake.readthedocs.io/en/stable/index.html">snakemake</a> are installed.</li> </ul> <p>The simulate-rnaseq.tar.gz&nbsp;archive can be re-executed on a vanilla machine that only has Conda and Snakemake installed via:</p> <pre><code class="language-bash">tar -xf simulate-rnaseq.tar.gz snakemake --use-conda -n</code></pre> <p>&nbsp;</p> <p>&nbsp;</p>