| This tool is part of the workflow **PAQmiR** for the *Prediction Annotation and Quantification of miRNA with miRDeeThe module maps the deep sequencing reads to predefined miRNA precursors and determines by that the expression of the corresponding miRNAs.
This wrapper was forked from the rbc_mirdeep2_quantifier wrapper of the RNA-Bioinformatics network ==> https://www.denbi.de/network/rna-bioinformatics-center-rbc ==> https://github.com/bgruening First, the predefined mature miRNA sequences are mapped to the predefined precursors. Optionally, predefined star sequences can be mapped to the precursors too. By that the mature and star sequence in the precursors are determined. Second, the deep sequencing reads are mapped to the precursors. The number of reads falling into an interval 2nt upstream and 5nt downstream of the mature/star sequence is determined. Modifications are the product of Valentin Marcon & Sylvain Marthey (Thanks to INRA Migale, IFB ressources & INRA GABI) |
hg clone https://toolshed.g2.bx.psu.edu/repos/smarthey/paqmir_mirdeep2_quantifier
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| fast quantitation of reads mapping to known miRBase precursors | 2.1.0 | 16.01 | |