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QuickMIRSeq: a pipeline for quick and accurate quantification of both known miRNAs and isomiRs by jointly processing multiple samples from microRNA sequencing

Shanrong Zhao, William Gordon, Sarah Du, Chi Zhang, Wen He, Li Xi, Sachin Mathur, Michael Agostino, Theresa Paradis, David von Schack, Michael Vincent, Baohong Zhang
2017 BMC Bioinformatics  
We implemented a pipeline called QuickMIRSeq for accurate quantification of known miRNAs and miRNA isoforms (isomiRs) from multiple samples simultaneously.  ...  Although many open-source tools for microRNA (miRNA)-seq data analyses are available, challenges remain in accurate miRNA quantification from large-scale miRNA-seq dataset.  ...  Availability of data and materials Project name: QuickMIRSeq pipeline Project home page: http://QuickMIRSeq.sourceforge.net Programming languages: Bash scripting, Perl, R, JavaScript Dependencies: Perl  ... 
doi:10.1186/s12859-017-1601-4 pmid:28320324 pmcid:PMC5359966 fatcat:s2czg5nswjdvdk5bguf6rzvdtm