Tools and best practices for data processing in allelic expression analysis.
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ABSTRACT:
SUBMITTER: Castel SE
PROVIDER: S-EPMC4574606 | biostudies-literature | 2015 Sep
REPOSITORIES: biostudies-literature
Publications
Tools and best practices for data processing in allelic expression analysis.
Castel Stephane E SE Levy-Moonshine Ami A Mohammadi Pejman P Banks Eric E Lappalainen Tuuli T
Genome biology 20150917
Allelic expression analysis has become important for integrating genome and transcriptome data to characterize various biological phenomena such as cis-regulatory variation and nonsense-mediated decay. We analyze the properties of allelic expression read count data and technical sources of error, such as low-quality or double-counted RNA-seq reads, genotyping errors, allelic mapping bias, and technical covariates due to sample preparation and sequencing, and variation in total read depth. We pro ...[more]
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