miRNA-MATE is a package designed specifically for mapping and summarizing miRNA (and isomiR) data from SOLiD sequencing data sets. MicroRNAs can be particularly challenging to map because of the limited information content in a 22nt molecule.
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Nicole Cloonan,et al.
MicroRNAs and their isomiRs function cooperatively to target common biological pathways.
Genome Biology 2011, 12:R126