Yanagi: transcript segment library construction for RNA-seq quantification

DOI10.4230/LIPICS.WABI.2017.10zbMATH Open1443.92139MaRDI QIDQ5111803FDOQ5111803

Authors: Mohamed K. Gunady, Steffen Cornwell, Stephen M. Mount, Héctor Corrada Bravo 

Publication date: 27 May 2020

Recommendations

• Comparing segmentation methods for genome annotation based on RNA-seq data
• SpliceTAPyR -- an efficient method for transcriptome alignment
• Exact transcript quantification over splice graphs
• Quantifying alternative splicing from paired-end RNA-sequencing data
• Deconvolution of base pair level RNA-seq read counts for quantification of transcript expression levels

zbMATH Keywords

RNA-seqgenome sequencingdifferential alternative splicingk-mer alignmenttranscriptome quantification

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Computational methods for problems pertaining to biology (92-08)

Cites Work

• Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments

Cited In (2)

• SpliceTAPyR -- an efficient method for transcriptome alignment
• Yanagi

Uses Software

• Voom
• TopHat
• RSEM
• Bowtie 2
• Salmon
• RapMap

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