Description Usage Format Details Source
A dataset containing alternative and reference allele read counts per cell and heterozygous variant, derived from a single-cell RNA-seq dataset of fibroblast and liver cells from crossed CAST/EiJ x C57BL/6J mouse strains. The dataset has been subsetted to 300 genes to restrict its size.
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An acset with four elements, featdata, refcount, altcount and
phenodata, see new_acset
for a description of these elements.
The acset contains data for 3313 variants and 336 single cells.
Allele counts were generated by alignment of the RNA-seq data to each of the
genomes of the two mouse strains and subsequently running samtools mpileup
using variants that were homozygous within each strain and differed
between the strain-genomes. Variants were filtered on being within RefSeq
genes. Variants were further filtered using the allele count data to not
monoallelically express the same allele across cells (see
filter_homovars
) and on having imbalanced allelic expression in
at least 3 cells (see filter_var_gt
. Features were filtered on
having at least two such variants (see filter_feat_nminvar
).
For additional filters and further details on the generation of the allele
count data see the Supplemental Data in Edsgard et al, scphaser: Haplotype
Inference Using Single-Cell RNA-Seq Data, Bioinformatics, 2016.
RNA-seq data can be found at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75659
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