A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing

<p>This is a public repository containing secondary datasets described in the publication <a href="https://doi.org/10.26508/lsa.202302481">"A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing"</a>. Primary data for this project are available at NCBI/SRA under the BioProject accession numbers PRJNA600820 and PRJNA834955, and include the following sequencing datasets:</p> <p>REH cell line:</p> <ul> <li>PacBio WGS</li> <li>ONT Ultralong WGS</li> <li>Illumina short-read PCR-free WGS</li> <li>IsoSeq RNA-seq</li> <li>Illumina short-read RNA-seq</li> </ul> <p>GM12878 cell line:</p> <ul> <li>Illumina short-read RNA-seq</li> </ul> <p>This dataset includes the following files:</p> <p><strong>Depth of Coverage analysis</strong></p> <ul> <li>Output from `samtools coverage`: <em>samtools.coverage.illumina.txt, samtools.coverage.ont.txt, samtools.coverage.pb.txt</em></li> <li>Output from `copycat` (binned coverage):&nbsp;<em>copycat.ont.coverage.10kb.csv, copycat.pb.coverage.10kb.csv, copycat.pcrfree.coverage.10kb.csv</em></li> </ul> <p><strong>Structural Variant (SV) callsets</strong></p> <ul> <li><strong>Raw:</strong>&nbsp;<em>illumina.tiddit.vcf, ont.sniffles.vcf, pb.sniffles.vcf</em></li> <li><strong>Filtered: </strong><em>REH.svs.filtered.csv</em></li> </ul> <p><strong>SNV callsets</strong></p> <ul> <li><strong>Filtered and annotated:</strong> <em>REH.mutect.filtered.ann.vcf.gz</em></li> </ul> <p><strong>Fusion gene callsets</strong></p> <ul> <li><strong>Short-read:&nbsp;</strong><em>GM12878.fusionreport.txt, illumina.all.txt, illumina.filtered.csv, REH.arriba.fusions.tsv, REH.fusioncatcher.fusion-genes.txt, REH.pizzly.txt, REH.squid.fusions.annotated.txt, REH.starfusion.abridged.tsv, REH.pdf</em></li> <li><strong>Long-read:&nbsp;</strong><em>cupcake.long.csv, cupcake.std.csv, jaffa_results.csv</em></li> <li><strong>Filtered: </strong><em>REH.fusions.filtered.csv</em><br>&nbsp;</li> </ul> <p>&nbsp;</p>