Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore technologies reveals platform-specific error patterns (repository for Genome Research paper, 2022)

<p>Simulated ONT and PacBio RNA-Seq data for &quot;Sequencing of individual barcoded cDNAs on Pacific Biosciences and Oxford Nanopore technologies reveals platform-specific error patterns&quot; paper (Mikheenko et al., Genome Research, 2022). All&nbsp;details can be found in the Methods section of the paper.</p> <p><strong>PacBio.simulated_uniform_coverage.fasta.gz</strong>&nbsp;and <strong>ONT.simulated_uniform_coverage.fasta.gz&nbsp;files</strong> were used in&nbsp;Supplemental Note &ldquo;Benchmarking of the read-to-isoform assignment algorithm&rdquo;.</p> <p><strong>ONT.simulated_real_expression.fasta.gz</strong>&nbsp;file and all GTF files were used in the Section &quot;Splice site correction improves transcript discovery precision&quot;.&nbsp;<strong>mouse.gencode.M26.spatial.15percent.reduced.gtf</strong>&nbsp;was used as the annotation file for all tools.&nbsp;<strong>mouse.gencode.M26.spatial.15percent.expressed.gtf </strong>contains the set of all expressed isoforms.&nbsp;<strong>mouse.gencode.M26.spatial.15percent.expressed_kept.gtf</strong> contains those&nbsp;of the&nbsp;isoforms that are in presented in the annotation file (&quot;known&quot; transcripts),&nbsp;<strong>mouse.gencode.M26.spatial.15percent.reduced.gtf</strong> contains expressed isoforms that were removed from the annotation&nbsp;(&quot;novel&quot; transcripts).</p>