Tool: SPAR: Web server and scripts for small RNA, short total RNA, miRNA-seq and single-cell small RNA sequencing data processing, analysis, and comparison with DASHR and ENCODE >180 tissues/cell types
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2.5 years ago by
pkuksa40 wrote:

A web server for interactive analysis and a set of scripts and modules for small RNA-seq, short total RNA-seq, miRNA-seq, single-cell small RNA-seq data processing, analysis, annotation, visualization, and comparison against reference ENCODE and DASHR datasets across >180 human tissues/cell types.

SPAR web server:

SPAR repository with the scripts (command line interface):

Distinctive key features:

  • Ab initio (annotation-free) small non-coding RNA (sncRNA) discovery and characterization across all major small RNA classes (miRNA, piRNA, snoRNAs, scRNAs, snRNAs, tRNAs, tRFs) and novel small RNA loci.
  • Expression comparison of user data with >180 reference human tissues, cell types and cell lines from DASHR and ENCODE
  • Annotations for GRCh37/hg19, GRCh38/hg38, and mm10 references genomes
  • Interactive sncRNA expression/annotation table for data exploration
  • Analyze public small RNA datasets
  • Analyze your own small RNA data

Supported file formats:

  • raw sequencing reads (FASTQ)
  • mapped reads (BAM)
  • genome-wide coverage tracks (BigWig)

Supported sequencing protocols:

  • small RNA-seq
  • miRNA-seq
  • short total RNA-seq
  • single cell small RNA-seq


SPAR has been published in Nucleic Acids Research.

Pavel P. Kuksa, Alexandre Amlie-Wolf, Zivadin Katanic, Otto Valladares, Li-San Wang, Yuk Yee Leung. SPAR: small RNA-seq portal for analysis of sequencing experiments. NAR 2018 (Web Server issue).

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