PMC

SPAR inputs. SPAR can be used to interactively process and analyze small RNA sequencing datasets. The user can select the input dataset from one of the publicly available DASHR/ENCDODE datasets (‘Analyze public datasets’, left box) or provide their own custom data via web-accessible URL or direct upload (‘Analyze your own data’, right box). SPAR parameters can be specified under ‘Additional analysis options’. Genomic regions of interest can be provided by the user under ‘Specify regions of interest’ section.

The SPAR workflow. Given a reference genome and input small RNA-seq dataset (custom or reference data), SPAR processes the small RNA-seq dataset and identifies sncRNA loci using unsupervised segmentation. sncRNA loci are grouped into the major small RNA classes or the novel unannotated category (total of 10 classes) and annotated with various genomic features. The SPAR results are summarized in interactive tables at the per locus and genome-wide level and are compared with reference ENCODE and DASHR tissues and cell lines. All results are available for download in a variety of formats.

SPAR outputs: (A) results can be downloaded easily as a single file (ZIP archive) or report (PDF). Individual files are available for download under ‘Download results’ section on the report page; (B) summary of the overall composition of the small RNA-seq data; (C) SPAR allows user to view, filter and download selected loci using the interactive sncRNA table; (D) SPAR provides overview of expression patterns across all loci in the small RNA sequencing data; (E) SPAR displays the variety of specific processing patterns across all loci in the small RNA sequencing data; (F) SPAR provides direct comparison of user data against ENCODE/DASHR reference tissues (RPM expression values).