MIRPIPE

MIRPIPE performs identification and quantification of microRNAs (miRNAs) and isomiRs from raw RNA-Seq reads to support miRNA profiling across sequencing platforms and in organisms lacking genome references.

Key Features:

• Automatic trimming of RNA-Seq reads: Trims raw RNA-Seq reads from multiple sequencing platforms to ensure compatibility across experimental setups.
• IsomiR processing: Processes isomiRs (sequence or length variants of miRNAs) to capture miRNA sequence heterogeneity.
• Quantification against reference databases: Quantifies detected miRNAs using public databases or user-uploaded reference datasets.

Scientific Applications:

• miRNA identification and quantification: Identifies and quantifies miRNAs that regulate gene expression in eukaryotic organisms.
• Analysis without genomic dependency: Enables miRNA analysis without genomic data dependency, expanding miRNA study scope to non-genomic model organisms.

Methodology:

Performs automatic trimming of raw RNA-Seq reads, processes isomiRs, and quantifies miRNAs against public databases or user-uploaded reference datasets; implemented in Perl and integrated into the Galaxy platform.