title: Tools and best practices for data processing in allelic expression analysis.
abstract: 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 provide guidelines for correcting such errors, show that our quality control measures improve the detection of relevant allelic expression, and introduce tools for the high-throughput production of allelic expression data from RNA-sequencing data.
authors.affiliation: New York Genome Center, New York, NY, USA. scastel@nygenome.org.|Department of Systems Biology, Columbia University, New York, NY, USA. scastel@nygenome.org.
authors.forename: Stephane E
authors.initials: SE
authors.lastname: Castel
authors.affiliation: Broad Institute, Cambridge, MA, USA.
authors.forename: Ami
authors.initials: A
authors.lastname: Levy-Moonshine
authors.affiliation: New York Genome Center, New York, NY, USA.|Department of Systems Biology, Columbia University, New York, NY, USA.
authors.forename: Pejman
authors.initials: P
authors.lastname: Mohammadi
authors.affiliation: Broad Institute, Cambridge, MA, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Banks
authors.affiliation: New York Genome Center, New York, NY, USA. tlappalainen@nygenome.org.|Department of Systems Biology, Columbia University, New York, NY, USA. tlappalainen@nygenome.org.
authors.forename: Tuuli
authors.initials: T
authors.lastname: Lappalainen
mesh_terms: D000483:Alleles; D002460:Cell Line; D003627:Data Interpretation, Statistical; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods* / Q000592:standards; D060005:Genotyping Techniques / Q000592:standards; D006801:Humans; D017423:Sequence Analysis, RNA; D012984:Software