TY - JOUR
T1 - A Conceptual Framework for Abundance Estimation of Genomic Targets in the Presence of Ambiguous Short Sequencing Reads
AU - Górzcak, Katarzyna
AU - Claesen, Jürgen
AU - Burzykowski, Tomasz
N1 - Score=10
PY - 2019/12/31
Y1 - 2019/12/31
N2 - RNA sequencing (RNA-seq) is widely used to study gene-, transcript-, or exon expression. To quantify the expression level, millions of short sequenced reads need to be mapped back to a reference genome or transcriptome. Read mapping makes it possible to find a location to which a read is identical or similar. Based upon this alignment, expression summaries, that is, read counts are generated. However, reads may be matched to multiple locations. Such ambiguously mapped reads are often ignored in the analysis, which is a potential loss of information and may cause bias in expression estimation. We present the general principles underlying multiread allocation and unbiased estimation of the expression level of genes, exons, or transcripts in the presence of multiple mapped reads. The underlying principles are derived from a theoretical concept that identifies important sources of information such as the number of uniquely mapped reads, the total target length, and the length of the shared target regions. We show with simulation studies that methods incorporating some or all of the aforementioned sources of information estimate the expression levels of genes, exons, and/or transcripts with a higher precision and accuracy than methods that do not use this information. We identify important sources of information that should be taken into account by methods that estimate the abundance of genes, exons, and/or transcripts to achieve good precision and accuracy.
AB - RNA sequencing (RNA-seq) is widely used to study gene-, transcript-, or exon expression. To quantify the expression level, millions of short sequenced reads need to be mapped back to a reference genome or transcriptome. Read mapping makes it possible to find a location to which a read is identical or similar. Based upon this alignment, expression summaries, that is, read counts are generated. However, reads may be matched to multiple locations. Such ambiguously mapped reads are often ignored in the analysis, which is a potential loss of information and may cause bias in expression estimation. We present the general principles underlying multiread allocation and unbiased estimation of the expression level of genes, exons, or transcripts in the presence of multiple mapped reads. The underlying principles are derived from a theoretical concept that identifies important sources of information such as the number of uniquely mapped reads, the total target length, and the length of the shared target regions. We show with simulation studies that methods incorporating some or all of the aforementioned sources of information estimate the expression levels of genes, exons, and/or transcripts with a higher precision and accuracy than methods that do not use this information. We identify important sources of information that should be taken into account by methods that estimate the abundance of genes, exons, and/or transcripts to achieve good precision and accuracy.
KW - Abundance estimation
KW - multireads
KW - next-generation sequencing
UR - http://ecm.sckcen.be/OTCS/llisapi.dll/open/36889787
U2 - 10.1089/cmb.2019.0272
DO - 10.1089/cmb.2019.0272
M3 - Article
SN - 1557-8666
VL - 27
SP - 1
EP - 16
JO - Journal of Computational Biology
JF - Journal of Computational Biology
IS - 0
ER -