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
4
gravatar for pkuksa
10 months ago by
pkuksa40
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:

https://www.lisanwanglab.org/SPAR

SPAR repository with the scripts (command line interface):

https://bitbucket.org/account/user/wanglab-upenn/projects/SPAR

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

Citation:

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

ADD COMMENTlink written 10 months ago by pkuksa40

Please consider shortening the title of this post.

ADD REPLYlink written 10 months ago by genomax64k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2336 users visited in the last hour