Event Analysis: Using Transcript Events To Improve Estimates of Abundance in RNA-seq Data

G3 : Genes - Genomes - Genetics
Jeremy R B NewmanLauren M McIntyre

Abstract

Alternative splicing leverages genomic content by allowing the synthesis of multiple transcripts and, by implication, protein isoforms, from a single gene. However, estimating the abundance of transcripts produced in a given tissue from short sequencing reads is difficult and can result in both the construction of transcripts that do not exist, and the failure to identify true transcripts. An alternative approach is to catalog the events that make up isoforms (splice junctions and exons). We present here the Event Analysis (EA) approach, where we project transcripts onto the genome and identify overlapping/unique regions and junctions. In addition, all possible logical junctions are assembled into a catalog. Transcripts are filtered before quantitation based on simple measures: the proportion of the events detected, and the coverage. We find that mapping to a junction catalog is more efficient at detecting novel junctions than mapping in a splice aware manner. We identify 99.8% of true transcripts while iReckon identifies 82% of the true transcripts and creates more transcripts not included in the simulation than were initially used in the simulation. Using PacBio Iso-seq data from a mouse neural progenitor cell model, EA detec...Continue Reading

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Citations

Nov 21, 2021·Diabetes·Morgan J SmithPatrick Concannon

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Datasets Mentioned

BETA
SRP101446

Methods Mentioned

BETA
RNA-seq
PCR
flow cytometry
ChIP-seq

Software Mentioned

MEM
eXpress
BWA
Ensembl
AceView
MegaBLAST
STAR
prepare
PacBio
BEDtools

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