SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data.

ABSTRACT:

Background

The popularity of massively parallel exome and transcriptome sequencing projects demands new data mining tools with a comprehensive set of features to support a wide range of analysis tasks.

Results

SeqGene, a new data mining tool, supports mutation detection and annotation, dbSNP and 1000 Genome data integration, RNA-Seq expression quantification, mutation and coverage visualization, allele specific expression (ASE), differentially expressed genes (DEGs) identification, copy number variation (CNV) analysis, and gene expression quantitative trait loci (eQTLs) detection. We also developed novel methods for testing the association between SNP and expression and identifying genotype-controlled DEGs. We showed that the results generated from SeqGene compares favourabl

SUBMITTER: Deng X 

PROVIDER: S-EPMC3148209 | biostudies-literature | 2011 Jun

REPOSITORIES: biostudies-literature