Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine Work Log 05/17 m i R N A q u a n t i f i c a t i o n b y m i R D e e p 2 , f u t u r e s e r v i c e r e q u i r e m e n t  

known miRNA mapping by miRDeep2 •  map clean reads to miRBase 19 by miRDeep2 •  collapse identical reads to one, reduce computing complexity •  map known mature form to precursors •  miR-21-3p/5p are from mir-21 •  miR-92a-2-5p & miR-92a-3p are from mir-92a-2 •  map clean reads to precursors •  In the end, it generates •  expression csv/html file •  mapping result file ( *.mrd ) Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 2 

Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 3 >hsa-let-7a-1 total read count 4547 hsa-let-7a-3p read count 86 hsa-let-7a-5p read count 4461 remaining read count 0 exp fffff5555555555555555555555fffffffffffffffffffffffffffff333333333333333333333fff pri_seq ugggaugagguaguagguuguauaguuuuagggucacacccaccacugggagauaacuauacaaucuacugucuuuccua pri_struct (((((.(((..((((((((((((((((...(((.....))).((....))....))))))))))))))))..)))))))) #MM seq_12764104_x33 .....ugagguaguagguuguau......................................................... 0 seq_14291004_x1 .....ugagguaguagguuguaAa........................................................ 1 seq_14600233_x1 .....ugagguaguagguuguaGa........................................................ 1 seq_13432490_x7 .....ugagguaguagguuguaua........................................................ 0 seq_14536046_x1 .....ugagguaguagguuguGua........................................................ 1 seq_13951289_x2 .....ugCgguaguagguuguauag....................................................... 1 seq_12126963_x103 .....ugagguaguagguuguauag....................................................... 0 seq_12994164_x20 .....ugagguaguagguuguauaguuG.................................................... 1 seq_14318800_x1 .....Ggagguaguagguuguauaguuu.................................................... 1 seq_14110225_x1 .....ugagguaguagguuguCuaguuu.................................................... 1 seq_14609328_x1 .....ugaggGaguagguuguauaguuuu................................................... 1 seq_14503431_x1 .....ugagguaguagguuguauaguuGu................................................... 1 seq_13640624_x4 .....ugagguaguagguuguauGguuuu................................................... 1 seq_14040897_x1 .....ugagguaguagguuguauaguuuu................................................... 0 seq_14216290_x1 ......gagguagGagguuguauaguuu.................................................... 1 seq_14273319_x1 ........................................................cuauacaaucuacugucu...... 0 seq_14151372_x1 ........................................................cuauacaaucuacugucuu..... 0 seq_12581353_x47 ........................................................cuauacaaucuacugucuuucU.. 1 seq_14068260_x1 ........................................................cuCuacaaucuacugucuuucc.. 1 seq_13200705_x12 ........................................................cuauacaaucuacugucuuucc.. 0 seq_14434061_x1 ........................................................cuauacaaucuacugucuuuccu. 0 seq_14252288_x1 ........................................................cuauacaaucuacugucuuucUu. 1 seq_13735724_x3 .........................................................uauacaaucuacugucuuuccu. 0 ( excerpt from miRBase.mrd ) precursor total count mature-3p count mature-5p count loop count # of collapsed reads mismatch, #MM 

Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 4 >hsa-mir-6723 total read count 76 hsa-miR-6723-5p read count 6 remaining read count 70 exp ffffffffff5555555555555555555555fffffffffffffffffffffffffffffffffffffffffffffffffffffffff pri_seq augcaucgggauaguccgaguaacgucggggcauuccggauaggccgagaaaguguugugggaagaaaguuagauuuacgccgaugaau pri_struct ...((((((...((((..(.(..(.(((.((((((((((.....))).))..))))).)))...)..).)..))))....))))))... #MM seq_14490248_x1 .......gggGuaguccgaguaacgucggggcauuc..................................................... 1 seq_13787981_x2 ........ggGuaguccgaguaacgucgggg.......................................................... 1 seq_14166885_x1 ........ggGuaguccgaguaacgucggggcauuccgga................................................. 1 seq_14614238_x1 .........gGuaguccgaguaacgucgggg.......................................................... 1 seq_13939325_x2 .........gGuaguccgaguaacgucggggc......................................................... 1 seq_13982976_x1 .........gGuaguccgaguaacgucggggcauuccgg.................................................. 1 seq_13163937_x14 .........gGuaguccgaguaacgucggggcauuccgga................................................. 1 seq_14307394_x1 ...........uaguccgaguaacgucggggcauuccgga................................................. 0 seq_14435107_x1 ...........uaguccgaguaacgucggggcauuccggauaggccga......................................... 0 seq_14255623_x1 ...........uaguccgaguaacgucggggcauuccggauaggccUaga....................................... 1 seq_14525311_x1 ............aguccgaguaacgucggggcauuc..................................................... 0 seq_13293318_x10 ............aguccgaguaacgucggggcauuccgA.................................................. 1 seq_13808751_x2 ............aguccgaguaacgucggggcauuccgga................................................. 0 seq_14053258_x1 ............aguccgaguaacgucggggcauuccggaGa............................................... 1 seq_13690859_x3 .............guccgaguaacgucggggcauuccgA.................................................. 1 seq_13812527_x2 .............guccgaguaacgucggggcauuccgga................................................. 0 seq_14417124_x1 ...............ccgaguaacgucggggcauuccggauagg............................................. 0 seq_14604682_x1 ..................aguaacgucggggcauuccggauaggA............................................ 1 seq_14044156_x1 ........................gucggggcauuccggaua............................................... 0 seq_14042326_x1 ........................gucggggcauuccggauaggccUaga....................................... 1 seq_14356501_x1 ...........................ggggcauuccggauaggccUagaaaguguugugg............................ 1 seq_14357983_x1 ...........................ggggcauuccggauaggccUagaaaguguugugggaagaaa..................... 1 seq_14202061_x1 ......................................gauaggccUagaaaguguugugggaagaaaguuagauuuacgccga..... 1 seq_14307625_x1 .......................................auaggccUagaaaguguugugggaagaaaguuagauuuac.......... 1 seq_14425118_x1 .........................................aggccUagaaaguguugugggaagaaaguuagau.............. 1 seq_14169043_x1 .........................................aggccUagaaaguguugugggaagaaaguuagauuuacgccga..... 1 seq_14505391_x1 .........................................aggccgagaaaguguugugggaagaaaguuagauuuacgccga..... 0 seq_14249343_x1 ..........................................ggccUagaaaguguugugggaagaaaguuagauuuacgccga..... 1 seq_14359223_x1 ...........................................gccUagaaaguguugugggaagaaaguuaga............... 1 seq_14203578_x1 ...........................................gccUagaaaguguugugggaagaaaguuagauuuacgccg...... 1 seq_14579921_x1 ...............................................agaaaguguugugggaag........................ 0 case having remained (loop) reads (excerpt from miRBase.mrd) 

Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 5 Future Service Requirement Software License, Python, R, GIT, HTML5+JS+D3 

Quick Software License Intro – MIT / GPL •  MIT license (BSD-like) •  Copyright Notice 著作權聲明 •  Disclaimer 免責聲明 •  compatible to GPL •  Python*, Apache, PostgreSQL, X11, … •  GPL v3 license (GPL-like) •  Copyleft 自由軟體的聖戰 •  公開程式碼 •  要用我的 code，就要用相容的 license (GPL)，不然就是商業授權 •  R and most R packages, GNU series (gcc, ReadLine, …) More on •  [BizLePro] 主題講座 #4：給資訊人的智財導論_20130429_richard by Yi-Feng Tzeng https://speakerdeck.com/yftzeng/bizlepro-zhu-ti-jiang-zuo-number-4-gei-zi-xun-ren-de-zhi-cai-dao-lun-20130429-richard •  Know Your Code 1.0.0 by Yi-Feng Tzeng https://github.com/yftzeng/KnowYourCode Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 6