mirGFF3
Define a GFF3 format for output of small RNA pipelines. Here, we present a community based, open source project to work toward the standardization of miRNA pipelines and encourage the development of downstream tools for visualization, differential expression, sample clustering, and model prediction analyses. This project is an international collaboration, with experts from different countries that have been developing miRNA pipelines and resources. We have described a standard format for the output of miRNA detection and quantification tools using small RNA-seq data. The format is based on the GFF3 standard in order to support reference coordinates and parent/child relationships between the features. The format contains information foreach sequence and its annotation to the miRNA precursor, the definition of reference or isomiR sequence, its quality, the isomiR type, and abundance in the data set. Moreover, we support a command line python tool to manage the miRNA GFF3 format (miRTop). Currently, miRTop can convert the output of commonly used small RNA-Seq pipelines, such as seqbuster, isomiR-SEA, sRNAbench, and Prost!, as well as BAM files to the miRNA GFF3 format. Importantly, the miRge pipeline has adapted the GFF3 format natively. miRTop can convert miRNA GFF3 files to a count matrix that can be easily imported to any downstream tool (i.e. for differential expression analysis).
Description
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Define a GFF3 format for output of small RNA pipelines. Here, we present a community based, open source project to work toward the standardization of miRNA pipelines and encourage the development of downstream tools for visualization, differential expression, sample clustering, and model prediction analyses. This project is an international collaboration, with experts from different countries that have been developing miRNA pipelines and resources. We have described a standard format for the output of miRNA detection and quantification tools using small RNA-seq data. The format is based on the GFF3 standard in order to support reference coordinates and parent/child relationships between the features. The format contains information foreach sequence and its annotation to the miRNA precursor, the definition of reference or isomiR sequence, its quality, the isomiR type, and abundance in the data set. Moreover, we support a command line python tool to manage the miRNA GFF3 format (miRTop). Currently, miRTop can convert the output of commonly used small RNA-Seq pipelines, such as seqbuster, isomiR-SEA, sRNAbench, and Prost!, as well as BAM files to the miRNA GFF3 format. Importantly, the miRge pipeline has adapted the GFF3 format natively. miRTop can convert miRNA GFF3 files to a count matrix that can be easily imported to any downstream tool (i.e. for differential expression analysis).
metasource: Fairsharing.orgversion: None
Webpage:
https://github.com/miRTop/mirGFF3Webpage
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Licence:
Name: mirGFF3 MIT License DocumentLicence name
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micro rna
metasource: Fairsharing.org
version: None
rna sequencing
metasource: Fairsharing.org
version: None
Tags
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micro rna
metasource: Fairsharing.orgversion: None
rna sequencing
metasource: Fairsharing.orgversion: None
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