Transcriptome, metaranscriptome, and translatome data for RIBOSS

<p>This record contains long- and short-read sequence alignment files&nbsp;to test <a href="https://github.com/lcscs12345/riboss">RIBOSS</a>.</p> <p>To reproduce the results in&nbsp;<a href="https://github.com/lcscs12345/riboss_paper/blob/master/jupyter_notebooks/styphimurium.ipynb">styphimurium.ipynb</a>, clone the <a href="https://github.com/lcscs12345/riboss_paper">RIBOSS_paper</a> repository, and create a&nbsp;<code>conda</code> environment according to <code>README</code>.</p> <p>Create new directories&nbsp;<code>mkdir -p doc/ doc/metatranscriptome doc/styphimurium/ doc/styphimurium/rnaseq doc/styphimurium/riboseq</code>.</p> <p>Download the alignment files for <em>S. enterica</em> transcriptome and metatranscriptome (a cocktail of&nbsp;<em>S. enterica</em> serovar Enteritidis, <em>Escherichia coli</em> O157:H7, and <em>Listeria monocytogenes</em>).</p> <ul> <li>SRR11215003.bam and SRR11215004.bam: Nanopore long-read direct RNA-seq. Download and&nbsp;<code>mv SRR24781620.bam doc/metatranscriptome</code>.</li> <li>SRR11215663.bam and SRR11215664.bam: Illumina short-read RNA-seq. Download and&nbsp;<code>mv SRR24781620.bam doc/metatranscriptome</code>.</li> <li>SRR24781620.bam: Nanopore long-read cDNA sequencing. Download and&nbsp;<code>mv SRR24781620.bam doc/styphimurium/rnaseq</code>.</li> </ul> <p>Download <em>S. enterica</em> serovar Typhimurium ribosome profiling data and <code>mv ERR913094*.out.bam doc/styphimurium/riboseq</code>.</p> <ul> <li><code>ERR9130942Aligned.out.bam</code>: RNase I, 1000 U.</li> <li><code>ERR9130943Aligned.out.bam</code>: RNase I, 500 U.</li> <li><code>ERR9130946Aligned.out.bam</code>: matched RNA-seq.</li> </ul>