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Atul Kakrana edited this page Mar 11, 2017 · 4 revisions

sPARTA : Small RNA-PARE Target Analyzer

NOTE: This wiki is a work in progress

updated : 01/01/2017
version : 1.22
release : https://github.com/atulkakrana/sPARTA/releases
citation : [Kakrana, A., Hammond, R., Patel, P., Nakano, M. & Meyers, B. C. sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software. Nucleic Acids Res. gku693– (2014). doi:10.1093/nar/gku693] (https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gku693)

###Description

small RNA-PARE Target Analyzer (sPARTA) is a tool which utilizes high-throughput sequencing to profile genome-wide cleavage products. sPARTA begins with a built-in parallelized target prediction module for plant miRNAs called miRferno. sPARTA as a whole utilizes multi-core servers to achieve two-dimensional parallelization in order to maintain a low memory footprint, imperative to achieve a full genome analysis.

Dependencies

sPARTA requires a few additional tools or python3 libraries to work properly:

  1. bowtie2 - It can be downloaded from authors [page] (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml).After installation it must be added to $PATH variable so that it can bee accessed directly.

  2. Two python3 modules, used generally for scientific computations:
    numpy - http://www.numpy.org/
    scipy - http://www.scipy.org/

Both 'numpy' and 'scipy' may easily be installed using (Python) PIP. Check this page on how to install PIP. https://pip.pypa.io/en/stable/installing.html

Please contact author [here] (https://github.com/atulkakrana/sPARTA/issues) for any further questions or issues

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