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 |