Given a set of aligned reads in 1 or more .sam files, produce an annotated version of the .sam where each read is given an annotation based on its coordinate. Additional summary information about the content of each sample is also generated, including miRNA species and other genomic features found.
Based on analysis software used in Morin et al., Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells., Genome Research Apr, 2008.
Documentation on required applications and instructions for running the software is in the README.TXT in the tarball.
This software is further described in: Large-scale profiling of microRNAs for The Cancer Genome Atlas. Chu A, Robertson G, Brooks D, Mungall AJ, Birol I, Coope R, Ma Y, Jones S, Marra MA. Nucleic Acids Res. 2015 Aug 13. pii: gkv808. [Epub ahead of print] PMID: 26271990
Author: Andy Chu
For support and other inquiries, contact Denise Brooks.
Releases of this project are made on GitHub. Please visit the mirna GitHub project for stable releases as well as access to the source tree.
Please be aware that the end coordinate in the isoform.txt, produced by the miRNA pipeline, is exclusive (i.e. offset by 1) for all miRNA data processed before January 31, 2019, with pipeline versions 0.2.7 or earlier. The latest version of the code (v0.2.8) has been updated so that the end coordinate is inclusive.