We are analyzing https://link.springer.com/article/10.1186/s12859-015-0800-0.

Title:
tDRmapper: challenges and solutions to mapping, naming, and quantifying tRNA-derived RNAs from human small RNA-sequencing data | BMC Bioinformatics
Description:
Background Small RNA-sequencing has revealed the diversity and high abundance of small RNAs derived from tRNAs, referred to as tRNA-derived RNAs. However, at present, there is no standardized nomenclature and there are no methods for accurate annotation and quantification of these small RNAs. tRNA-derived RNAs have unique features that limit the utility of conventional alignment tools and quantification methods. Results We describe here the challenges of mapping, naming, and quantifying tRNA-derived RNAs and present a novel method that addresses them, called tDRmapper. We then use tDRmapper to perform a comparative analysis of tRNA-derived RNA profiles across different human cell types and diseases. We found that (1) tRNA-derived RNA profiles can differ dramatically across different cell types and disease states, (2) that positions and types of chemical modifications of tRNA-derived RNAs vary by cell type and disease, and (3) that entirely different tRNA-derived RNA species can be produced from the same parental tRNA depending on the cell type. Conclusion tDRmappernot only provides a standardized nomenclature and quantification scheme, but also includes graphical visualization that facilitates the discovery of novel tRNA and tRNA-derived RNA biology.
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Keywords {🔍}

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Topics {✒️}

user-driven post-hoc quantification small rna-seq data article download pdf trna-derived small rnas small trna-derived rnas pre-trna-derived tdr profile trna-derived rna fragments small rna-seq reads small rna-seq datasets performed small rna-seq quantifying trna-derived rnas trna-derived rna profiles specific trna-derived rnas small rna-sequencing median pair-wise r2 = 0 trna-derived rna species trna-derived rna biology color-coded structure post-transcriptional rna modifications fast gapped-read alignment small rna-seq nascent pre-trna transcripts transfer rna modifications trna-derived rnas vary coding rnas demonstrates tissue-specific profiles multi-copy trna genes small rnas derived automatically generates visualization h1-derived mesendoderm cells chronic viral hepatitis small degraded fragments pre-arg-ctc-2-1-trh-1 deep sequencing data small rna fields glu-ctc-1-7-trh-da glu-ctc-2-1-trh-da bmc bioinformatics 16 human cell type/tissue smaller search space �pre-w-x-y primary tissue/fluid samples trna-val-cac-1-6 accounts facilitate future research future research overturns human cell types/tissues h1-derived mesendoderm sample privacy choices/manage cookies full access trna-derived rnas

Schema {🗺️}

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      description:Small RNA-sequencing has revealed the diversity and high abundance of small RNAs derived from tRNAs, referred to as tRNA-derived RNAs. However, at present, there is no standardized nomenclature and there are no methods for accurate annotation and quantification of these small RNAs. tRNA-derived RNAs have unique features that limit the utility of conventional alignment tools and quantification methods. We describe here the challenges of mapping, naming, and quantifying tRNA-derived RNAs and present a novel method that addresses them, called tDRmapper. We then use tDRmapper to perform a comparative analysis of tRNA-derived RNA profiles across different human cell types and diseases. We found that (1) tRNA-derived RNA profiles can differ dramatically across different cell types and disease states, (2) that positions and types of chemical modifications of tRNA-derived RNAs vary by cell type and disease, and (3) that entirely different tRNA-derived RNA species can be produced from the same parental tRNA depending on the cell type. tDRmappernot only provides a standardized nomenclature and quantification scheme, but also includes graphical visualization that facilitates the discovery of novel tRNA and tRNA-derived RNA biology.
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         Algorithms
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