Transcriptomics: quantifying non-uniform read distribution using MapReduce

DOI10.1142/S0129054118430086MaRDI QIDQ5384628zbMATH OpenOpenAlexWikidataFDO

Authors Jamie J. Alnasir, Hugh P. Shanahan

Publication date 24 June 2019

Published in International Journal of Foundations of Computer Science (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1142/s0129054118430086

zbMATH Keywords

4-mersDrosophilaMapReducemotif analysisRNA-seqtranscriptomics

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20)

Recommendations

• Deconvolution of base pair level RNA-seq read counts for quantification of transcript expression levels
• Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates
• A penalized likelihood approach for robust estimation of isoform expression
• Quantifying alternative splicing from paired-end RNA-sequencing data
• Removing technical variability in RNA-seq data using conditional quantile normalization

Cites work

• Google's MapReduce programming model - Revisited
• scientific article; zbMATH DE number 50329 (Why is no real title available?)
• On the computational complexity of MapReduce

Cited in

(2)

• MATHT: a web server for comprehensive transcriptome data analysis
• Lognormality and oscillations in the coverage of high-throughput transcriptomic data towards gene ends

Describes a project that uses

Uses Software

• MPI
• Hadoop
• EDAseq

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