tinyRNA: precision analysis of small RNA-seq data with user-defined hierarchical selection rules

AJ Tate, KC Brown, TA Montgomery - BioRxiv, 2022 - biorxiv.org
BioRxiv, 2022biorxiv.org
ABSTRACT Summary tinyRNA performs precision analysis of small RNAs, including
miRNAs, piRNAs, and siRNAs, from high-throughput sequencing experiments. At the core of
tinyRNA is a highly flexible counting utility, tiny-count, that allows for hierarchical assignment
of small RNA reads to features based on positional information, extent of feature overlap,
5'nucleotide, length, and strandedness. tinyRNA provides an all-in-one solution for small
RNA-seq data analysis, with documentation and statistics generated at each step for …
Abstract
tinyRNA performs precision analysis of small RNAs, including miRNAs, piRNAs, and siRNAs, from high-throughput sequencing experiments. At the core of tinyRNA is a highly flexible counting utility, tiny-count, that allows for hierarchical assignment of small RNA reads to features based on positional information, extent of feature overlap, 5’ nucleotide, length, and strandedness. tinyRNA provides an all-in-one solution for small RNA-seq data analysis, with documentation and statistics generated at each step for accurate, reproducible results.
Availability and Implementation
tinyRNA tools are implemented in Python and R, and the pipeline workflow is coordinated with CWL. tinyRNA is free and open-source software distributed under the GPLv3 license. tinyRNA is available at https://github.com/MontgomeryLab/tinyRNA.
Contact
tai.montgomery@colostate.edu
Supplementary information
Reference data, including genome sequences and features tables, for certain species can be found at https://www.MontgomeryLab.org.
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