Dataset Information

Systematic Scatterometer Wind Errors Near Coastal Mountains.

ABSTRACT: Satellite scatterometers provide the only regular observations of surface wind vectors over vast swaths of the world oceans, including coastal regions, which are of great scientific and societal interest but still present challenges for remote sensing. Here we demonstrate systematic scatterometer wind errors near Hawaii's Big Island: Two counter-rotating lee vortices, which are clear in the International Comprehensive Ocean-Atmosphere Data Set ship-based wind climatology and in aircraft observations, are absent in the Jet Propulsion Laboratory and Remote Sensing Systems scatterometer wind climatologies. We demonstrate similar errors in the representation of transient Catalina Eddy events in the Southern California Bight. These errors likely arise from the nonuniqueness of scatterometer wind observations, that is, an "ambiguity removal" is required during processing to select from multiple wind solutions to the geophysical model function. We discuss strategies to improve the ambiguity selection near coastal mountains, where small-scale wind reversals are common.

SUBMITTER: Kilpatrick T

PROVIDER: S-EPMC6919418 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Publications

Systematic Scatterometer Wind Errors Near Coastal Mountains.

Kilpatrick Thomas T Xie Shang-Ping SP Tokinaga Hiroki H Long David D Hutchings Nolan N

Earth and space science (Hoboken, N.J.) 20191018 10

Satellite scatterometers provide the only regular observations of surface wind vectors over vast swaths of the world oceans, including coastal regions, which are of great scientific and societal interest but still present challenges for remote sensing. Here we demonstrate systematic scatterometer wind errors near Hawaii's Big Island: Two counter-rotating lee vortices, which are clear in the International Comprehensive Ocean-Atmosphere Data Set ship-based wind climatology and in aircraft observat ...[more]

PMID: 31894202

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Project description:While the importance of random sequencing errors decreases at higher DNA or RNA sequencing depths, systematic sequencing errors (SSEs) dominate at high sequencing depths and can be difficult to distinguish from biological variants. These SSEs can cause base quality scores to underestimate the probability of error at certain genomic positions, resulting in false positive variant calls, particularly in mixtures such as samples with RNA editing, tumors, circulating tumor cells, bacteria, mitochondrial heteroplasmy, or pooled DNA. Most algorithms proposed for correction of SSEs require a training data set, which is typically either from a part of the data set being M-bM-^@M-^\recalibratedM-bM-^@M-^] (Genome Analysis ToolKit, or GATK) or from a separate data set with special characteristics (SysCall). Here, we combine the advantages of these approaches by adding synthetic RNA spike-in standards to human RNA, and use GATK to recalibrate base quality scores with reads mapped to the spike-in standards. Compared to conventional GATK recalibration that uses reads mapped to the genome, spike-ins improve the accuracy of Illumina base quality scores by a mean of 5 units, and by as much as 13 units M-BM- at CpG sites. In addition, since reads mapping to the genome are not used for recalibration, our method allows run-specific recalibration even for the many species without a comprehensive and accurate SNP database. We also use GATK with the spike-in standards to demonstrate that the Illumina RNA sequencing runs overestimate quality scores for AC, CC, GC, GG, and TC dinucleotides, while SOLiD has less dinucleotide SSEs but more SSEs for certain cycles. We conclude that using these DNA and RNA spike-in standards with GATK improves base quality score recalibration. Four human RNA samples with equimolar ERCC spike-in standards were sequenced on Illumina. Two human brain/liver/muscle RNA mixtures with dynamic range of ERCC spike-in standards were sequenced on SOLiD.

Dataset Information

Systematic Scatterometer Wind Errors Near Coastal Mountains.

Publications

Systematic Scatterometer Wind Errors Near Coastal Mountains.

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