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|Alternative name||Quantitative Allele Specific Analysis of Reads|
|Interface||Command line interface|
|Restrictions to use||None|
|Operating system||Unix/Linux, Mac OS, Windows|
No version available
- person_outline Francesca Luca
- person_outline Roger Pique-Regi
Publications for Quantitative Allele Specific Analysis of Reads
Allele specific expression and methylation in the bumblebee, Bombus terrestris
[…] all the SNPs, before the SNPs were filtered based on mapping quality score (; ). Only SNPs with a mapping quality score of p < 0.05 and a read depth of ≥6 were included in the analyses.The R package, QuASAR implements a statistical method for: (1) genotyping from next-generation sequencing reads (according to the Hardy–Weinberg equilibrium), and (2) conducting inference on allele specific expressi […]
IDP ASE: haplotyping and quantifying allele specific expression at the gene and gene isoform level by hybrid sequencing
[…] hers (,,). However, either available phased genotypes (e.g. MMSEQ, asSeq and EMASE) or family trio data (e.g. AlleleSeq and Allim) are required for haplotyping using most of these applications. While QuASAR uses solely RNA-seq data, it can only perform ASE analysis at the single SNV level. MBASED is the only currently available tool for ASE analysis at the gene level using only RNA-seq data. Howev […]
Genetic and Transcriptional Analysis of Human Host Response to Healthy Gut Microbiota
[…] ollowing analysis.Using samtools mpileup and the hg19 human reference genome, we obtained the read counts at each SNP in each sample from the RNA-seq data. These pileups were then processed using the QuASAR package () by combining the RNA-seq reads from each sample (as they are all derived from the same colonocyte cell line) for joint genotyping. From the genotype information we identified heteroz […]
Which Genetics Variants in DNase Seq Footprints Are More Likely to Alter Binding?
[…] n of which genetic variants in DNaseI sensitive regions are more likely to affect binding. To experimentally assess the accuracy of our answer, we used Quantitative Allele-Specific Analysis of Reads (QuASAR)  to perform joint genotyping and ASH analysis within DNase I hypersensitivity (DHS) regions (). While the initial quality filtering is the same as for the CENTIPEDE analysis, the parameters […]
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