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

This is a public repository containing secondary datasets described in the publication "A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing". Primary data for this project are available at NCBI/SRA under the BioProject accession numbers PRJNA600820 and PRJNA834955, and include the following sequencing datasets:

REH cell line:

PacBio WGS

ONT Ultralong WGS

Illumina short-read PCR-free WGS

IsoSeq RNA-seq

Illumina short-read RNA-seq

GM12878 cell line:

Illumina short-read RNA-seq

This dataset includes the following files:

Depth of Coverage analysis

Output from `samtools coverage`: samtools.coverage.illumina.txt, samtools.coverage.ont.txt, samtools.coverage.pb.txt

Output from `copycat` (binned coverage): copycat.ont.coverage.10kb.csv, copycat.pb.coverage.10kb.csv, copycat.pcrfree.coverage.10kb.csv

Structural Variant (SV) callsets

Raw: illumina.tiddit.vcf, ont.sniffles.vcf, pb.sniffles.vcf

Filtered: REH.svs.filtered.csv

SNV callsets

Filtered and annotated: REH.mutect.filtered.ann.vcf.gz

Fusion gene callsets

Short-read: 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

Long-read: cupcake.long.csv, cupcake.std.csv, jaffa_results.csv

Filtered: REH.fusions.filtered.csv