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 https://www.lisanwanglab.org/SPAR/analyze-public-dataset
- Analyze your own small RNA data https://www.lisanwanglab.org/SPAR/analyze-own-data
Supported file formats:
- raw sequencing reads (FASTQ)
- mapped reads (BAM)
- genome-wide coverage tracks (BigWig)
Supported sequencing protocols:
- small RNA-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). https://doi.org/10.1093/nar/gky330