additional copy ofFADS2P1, which has been under positive selection, is an example that highlights the benefits of HQ haplotype-specific assemblies. TheFADS2P1gene region in both Brahman and Angus span ~1.4 Mb of sequence, while the twoFADS2P1genes ...
To perform gene expression deconvolution analysis, we used BRETIGEA (BRain cEll Type specIfic Gene Expression Analysis) [49]. The raw gene expression count matrix was input to BRETIGEA to estimate the proportions of neuronal and glial cell types present in the samples. These cell-type proportions...
We show that this workflow improves accuracy over state-of-the-art RNA sequencing mapping methods, and that it can efficiently quantify haplotype-specific transcript expression without needing to characterize the haplotypes of a sample beforehand....
a method to infer clone-specific and haplotype-specific CNAs from DNA sequencing data from one or more bulk tumor samples from the same patient (Fig.1). HATCHet2 has two key advantages over previous methods, including HATCHet. First, HATCHet2 identifiesmirrored-subclonal CNAs, which are events...
(Fig.3b). Interestingly, ASEGs from a common gene set also exhibited variable allele-specific expression patterns among tissues. For instance, of the 3149 ASEGs detected in two or more accessions across different haplotype assemblies, 72% exhibited tissue-specific expression patterns that varied ...
Haplotype-specific analysis, useful for eQTL analysis and studies of F1 crosses Multi-mapping of reads, including mapping to transcripts from different genes, is properly taken into account The insert size distribution is taken into account
In this paper, we present HapIso (Haplotype-specific Isoform Reconstruction), a method able to tolerate the relatively high error-rate of the single-molecule platform and partition the isoform reads into the parental alleles. Phasing the reads according to the allele of origin allows our method ...
SFB , a gene located in the S locus region, encodes an F-box protein that has appropriate S haplotype-specific variation to be the pollen determinant in the self-incompatibility reaction. This study characterizes SFBs of two self-compatible (SC) haplotypes, S 4' and S f , of Prunus . ...
(LD)22. The above mentioned haplotypes may be in close LD with the causal variant or may themselves consist of the causal variants of interest26. In addition, the biological functions of transcripts of specific tissues involved in the hypothalamic-pituitary-adrenal (HPA) axis from the same ...
In heterozygous genomes, allele-specific measurements can reveal biologically significant differences in DNA methylation between homologous alleles associated with local changes in genetic sequence. Current approaches for detecting such events from whole