Yanagi: transcript segment library construction for RNA-seq quantification

DOI10.4230/LIPICS.WABI.2017.10MaRDI QIDQ5111803zbMATH OpenFDO

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

Publication date 27 May 2020

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)

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

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

Describes a project that uses

Uses Software

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

This page was built for publication: Yanagi: transcript segment library construction for RNA-seq quantification

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q5111803)