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Table 1 miRNA quantification methods for small RNA-seq

From: miR-MaGiC improves quantification accuracy for small RNA-seq

Method Year Architecture miRNA search space Aligner Alignment to miRNAs Handling multi-mapped Reads Counts
CAP-miRSeq [3] 2014 Pipeline for Linux environ-ment miRBase mature and precursor Bowtie [24] Alignment within miRDeep2 [11] All valid mappings reported by miRDeep2 Use miRDeep2 for counts; for mature miRNAs with multiple precursors, return weighted counts for each precursor
Chimira [4] 2015 Web application miRBase precursors BLASTn [25] Max 2 mismatches User choice to keep the first match or assign fractional counts to all matches  
CPSS [5] 2012 Web application miRBase SOAP2 [26] By default, best hits with max 2 mismatches By default, report one random alignment per read  
iSRAP [6] 2015 Pipeline for Linux environment User defined Bowtie2 [27] Seed length 20; max 1 mismatch in seed Bowtie2 default: report one best alignment per read BEDTools [28]
miRanalyz- er [7] 2011 Web application miRBase mature, maturestar, unobserved maturestar, and hairpin Bowtie Seed length 17. By default, max 1 mismatch in seed By default, allow up to 10 mappings per read  
miRDeep2 quantifier [8] 2012 Perl script miRBase mature and precursor Bowtie By default, max 1 mismatch By default, all valid mappings Count all instances where a read maps to the same part of precursor as a mature miRNA
miRExpress [9] 2009 Command line tools miRBase; identical mature miRNAs collapsed Novel aligner based on Smith–Waterman algorithm [29] Find one best mapping per read. By default, keep those where read length is equal to miRNA length and identity is 100% Identify at most one mapping per read Count all valid mappings for each collapsed miRNA
miRge [10] 2015 Perl script miRBase mature and precursor; identical mature miRNAs collapsed; near-identical families merged after alignment Bowtie Sequential alignments: first perfect match, then up to 2 mismatches All valid mappings Counts per miRNA with identical and near identical miRNAs merged together
miRNAKey [11] 2010 Java GUI with Perl backend miRBase mature or precursor BWA [30] User defined max edit distance Optionally use SEQ-EM [31] to optimize distribution of multiply aligned reads Optimized distribution of reads to miRNAs
mirTools 2.0 [12] 2013 Web application miRBase SOAP2 By default, best hits with max 2 mismatches By default, report one random alignment per read  
Oasis [13] 2015 Web application miRBase STAR [32] Max mismatches 5% of read length STAR default: report all alignments for reads with up to 10 mappings only Feature-Counts [33]
omiRAs [14] 2013 Web application miRBase Bowtie Max 2 mismatches, best stratum only Assign fractional counts for multiply mapped reads  
Shortran [15] 2012 Command line modules miRBase Bowtie User defined   
sRNAbench [16] 2014 Web application User defined Bowtie User defined User defined; by default, allow up to 10 mappings per read Two output files: one with all mappings counted; one with only one mapping counted per read
  1. Implementation details of several recently published methods for miRNA expression quantification from small RNA-seq