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The option “-g” means the tolerance range for mapping mature miRNA

Usage : analysis [-r reference sequence file] [-m mature miRNA information in precursor sequences] [-d alignment result directory] [-o output file name (expression)] [-t output file for comparing result,optional]

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The option “-g” means the tolerance range for mapping mature miRNA

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  1. Usage : analysis [-r reference sequence file] [-m mature miRNA information in precursor sequences] [-d alignment result directory] [-o output file name (expression)] [-t output file for comparing result,optional] -r reference sequence file (This file must be the same as the file used to do alignmentSIMD) -m mature miRNA information in precursor sequences (The format must be the same with miRExpress/data/hsa_miRNA.txt) -d alignment result directory (This directory need to be the same with the directory used to do alignmentSIMD) -o output file for alignment result -t output file for expression result -g tolerance range for mapping mature miRNA [optional, default:4] -l similarity between read length and mature miRNA [optional, default:0.8] -s precursor structure file [optional] The option “-g” means the tolerance range for mapping mature miRNA hsa-let-7a-1 UGGGAUGAGGUAGUAGGUUGUAUAGUUUUAGGGUCACACCCACCACUGGGAGAUAACUAUACAAUCUACUGUCUUUCCUA UGAGGUAGUAGGUUGUAUAGUU hsa-let-7a TGAGGTAGTAGGTTGTATAGTTT 5 TGAGGTAGTAGGTTGTATAGT 3 TGAGGTAGTAGGTTGTATAGTT 21 ATGAGGTAGTAGGTTGTATAGTT 10 This read has more one base in 5’end (Comparing with known miRNAs). Therefore, it’s tolerance range is 1. When we compute the expression of hsa-let-7a in hsa-let-7a-1, the reads which locate in tolerance range are summed. Therefore, the expression of hsa-let-7a in hsa-let-7a-1 is 39 (5+3+21+10).

  2. The example for hsa-let-7a hsa-let-7a-1 UGGGAUGAGGUAGUAGGUUGUAUAGUUUUAGGGUCACACCCACCACUGGGAGAUAACUAUACAAUCUACUGUCUUUCCUA UGAGGUAGUAGGUUGUAUAGUU hsa-let-7a TGAGGTAGTAGGTTGTATAGTTT 5 TGAGGTAGTAGGTTGTATAGT 3 TGAGGTAGTAGGTTGTATAGTT 21 ATGAGGTAGTAGGTTGTATAGTT 10 hsa-let-7a-2 AGGUUGAGGUAGUAGGUUGUAUAGUUUAGAAUUACAUCAAGGGAGAUAACUGUACAGCCUCCUAGCUUUCCU UGAGGUAGUAGGUUGUAUAGUU hsa-let-7a TGAGGTAGTAGGTTGTATAGTTT 5 TGAGGTAGTAGGTTGTATAGT 3 TGAGGTAGTAGGTTGTATAGTT 21 hsa-let-7a-3 GGGUGAGGUAGUAGGUUGUAUAGUUUGGGGCUCUGCCCUGCUAUGGGAUAACUAUACAAUCUACUGUCUUUCCU UGAGGUAGUAGGUUGUAUAGUU hsa-let-7a TGAGGTAGTAGGTTGTATAGTTT 5 TGAGGTAGTAGGTTGTATAGT 3 TGAGGTAGTAGGTTGTATAGTT 21 GGTGAGGTAGTAGGTTGTATAGTT 1 According to default parameters of “analysis”, the expression of hsa-let-7a in three precursors are hsa-let-7a-1,hsa-let-7a = 5+3+21+10 = 39 hsa-let-7a-2,hsa-let-7a = 5+3+21 = 29 hsa-let-7a-3,hsa-let-7a = 5+3+21+1 = 30

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