ncPRO-seq is a tool for annotation and profiling of ncRNAs from smallRNA sequencing data. It aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions in miRBase, piRBase, Rfam and repeatMasker, and regions defined by users. The ncPRO pipeline also has a module to identify regions significantly enriched with short reads that can not be classified as known ncRNA families.
- Support multiple Solexa, SOLiD, 454 raw reads, and Bam files
- Reads grouping strategy (distinct vs abundant reads)
- Quality control of raw and aligned reads
- Reads mapping using the Bowtie software
- More than 15 annotated organisms from mammals/metazoan to plants
- Flexible annotation and analysis on ncRNA families from RFAM, UCSC tRNA, piRBase and miRBase
- Annotation and analysis of repeats classes from RepeatMasker
- Support user defined annotation files (gff3)
- Detect regions significantly enriched with reads
- Settings of UCSC Genome Browser tracks for visualization
- Stand-alone/command line pipelinee and user-friendly interface
- PDF and HTML report
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