E-miR is an easy to use perl-based analysis pipeline which was developed to handle the sequencing data in several automated steps including data format conversion, 3′ adapter removal, genome alignment and annotation to non-coding RNA transcripts.
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BMC Genomics. 2010 Dec 20;11:716. doi: 10.1186/1471-2164-11-716.
New methods for next generation sequencing based microRNA expression profiling.
Buermans HP, Ariyurek Y, van Ommen G, den Dunnen JT, ‘t Hoen PA.