1.Precision Medicine - exSEEK
Finding exRNA/cfRNA biomarker panel for cancer diagnosis
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âââ genome
â âââ bed
â â âââ lncRNA.exon.bed
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sample_id label source sex library dataset
CRC-2124325 CRC P1 M reverse train
CRC-2211756 CRC P1 M reverse train
CRC-2276341 CRC P1 F reverse test
CRC-2277930 CRC P1 M reverse train
- metadataäžå ±å å«6åïŒæ¯åçå«ä¹è§£éåŠäž
- sample_id: æ ·æ¬idïŒæ¯äžªæ ·æ¬çidæ¯å¯äžç
- label: æ ·æ¬çæ çŸïŒä¹æ¯æä»¬å®é 颿µç对象
- source: æ ·æ¬æ¥æºçå»é¢
- sex: æ ·æ¬äŸäœçæ§å«
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- 泚æ small RNA æ°æ®åäžè¿°ç long RNA æ°æ®çå€çæ¹æ³äžåïŒbamç®åœäžæ¯æ¯äžªæ ·æ¬çreadså蜬åœç»mappingåŸå°çbamæä»¶(æåæ æåº)åbam indexïŒæä»¥å¯¹æ¯äžªæ ·æ¬éœäŒå¯¹åº9䞪bamæä»¶(miRNA,lncRNA,mRNA,piRNA,snoRNA,snRNA,srpRNA,tRNAåYRNAåèªå¯¹åºäžäžªbamæä»¶)ã诊è§äžæçâDifferent Mapping stratgies for small and long RNA-seq dataâ
- genomeç®åœäžæ¯æä»¬åšmappingæ¶äœ¿çšçåºåå对åºçbowtie2 index
metadata.txt
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sample id RNA Isolation batch library prepration day gel cut size selection label sex id stage dataset
Sample_1S1 2 22 7 CRC F GSM1825212 I train
Sample_1S10 3 24 1 CRC F GSM1825215 I train
Sample_1S11 3 24 2 CRC F GSM1825239 I test
Sample_1S12 3 25 7 CRC M GSM1825071 I train
- metadataäžå ±å å«9åïŒæ¯åçå«ä¹è§£éåŠäž:
- sample id: æ ·æ¬çŒå·ïŒå¯¹äºæ¯äžªæ ·æ¬æ¯å¯äžç
- RNA Isolation batch, library prepration day, gel cut size selectionäžåè®°åœäºå®éªæ¹æ¬¡çä¿¡æ¯
- label: æ ·æ¬çæ çŸïŒä¹æ¯æä»¬å®é 颿µç对象
- sex: æ ·æ¬äŸäœçæ§å«
- stage: è¿ç€åæçä¿¡æ¯
- id: GEOæ°æ®åºäžçæ ·æ¬id
- dataset: åèæ°æ®éçäžç§äººäžºååïŒæä»¬æäžéšåäººçæ°æ®çšæ¥åtrainingïŒ åŠäžéšåäººçæ°æ®çšæ¥å testãæ³šæïŒå¯¹äºæ¬æµè¯äžçè¿ç§èŸå°çæ°æ®éïŒæä»¬äžæšèçšè¿ç§äººäžºäžæ¬¡æ§åå traning å test çæ¹åŒãæŽå¥œçæ¹æ³åèäžæç âæ°æ®éååâã
long RNA-seq: é¿RNAå端æµåºçmappingåRNA-seqçåžžè§åææµçšæ¯èŸäžèŽïŒå³çšspliced aligner(æä»¬è¿é䜿çšçæ¯STAR)å°readsæ¯å¯¹å°åèåºå ç»hg38äžãæä»¥å¯¹äºé¿RNAæ°æ®,äžäžªæ ·æ¬å¯¹åºäžäžªbamæä»¶,bamæä»¶çrecordéœåšhg38çåæ äžãsmall RNA-seq: å°RNAæ°æ®éçreadsé¿åºŠæ¯èŸçïŒåŠæçŽæ¥åŸåºå ç»äžæ¯å¯¹å®¹æäº§ç倧éçmultiple mappingãæä»¥æä»¬è¿ééçšçæ¹æ³æ¯äººäžºç对äžåç±»åçRNAå®ä¹äžäžªäŒå çº§ïŒæè¿äžªäŒå çº§å æreadsåŸåäžç±»RNAçèœ¬åœæ¬åºåäžmapping(DNA-seq alignerå³å¯ïŒè¿éçšçæ¯bowtie2)ïŒåæunmapped readsåŸäžäžç±»RNAçèœ¬åœæ¬åºåäžmappingãè¿ç§"sequential mapping"æ¯å€çå°RNAæµåºæ°æ®çäžç§åžžè§çç¥ïŒå€§å®¶å¯ä»¥åè2019, Cell Systems, Joel Rozowsky et al., exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profilingè¿ç¯æç« ãäŒå 次åºçå®ä¹æäžå®çäž»è§æ§ïŒéåžžäŒç»æ³šéçå¯ä¿¡åºŠæ¯èŸé«çRNAç±»ååæä»¬åšç ç©¶äžæ¯èŸå ³æ³šçRNAç±»åèŸé«çäŒå åºŠïŒæä»¬è¿ééçšçé¡ºåºæ¯miRNA,lncRNA,mRNA,piRNA,snoRNA,snRNA,srpRNA,tRNA,YRNAãå¯¹äºæ¯äžäžªå°RNAæµåºæ ·æ¬ïŒæä»¬éœäŒæäŸå€äžªbamæä»¶ïŒå¯¹åºäžåçRNAç±»åïŒæ¯äžäžªbamæä»¶çrecordéœåšçžåºçèœ¬åœæ¬åºåçåæ äžã
- æäº€äžä»œå®æŽçå·¥äœæ¥å(äžè±æäžé)ïŒæäŸäž»èŠç代ç ã
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- çšfeatureCountäžç±»çå·¥å ·ç»è®¡æ¯äžªåºå çread countsã
- æ ¹æ®bamæä»¶è®¡ç®åšæä»¬èèçRNAäžïŒäžåRNAç±»å(äŸåŠå¯ä»¥æmRNA,lncRNA,snoRNA,snRNA,srpRNA,tRNA,YRNA,pseudogeneåintronæ¥ååïŒè¯·åèhelpäžççžå ³ä»ç»)æå çæ¯äŸã
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metadata.txt
äžå·²æ æïŒåšcountæ¶éèŠäœ¿çšçžåºçåæ°ã- small RNA:
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scripts/count-transcripts.py
çšæ¥ç»è®¡æ¯äžäžªèœ¬åœæ¬äžæå€å°readsãåšåºæ¬çåæäžæä»¬å»ºè®®å€§å®¶åªèèmiRNAåpiRNAïŒæŽå€çåæå¯ä»¥åçäžé¢ç "Part IV Optional Tasks". - æäžåæ ·æ¬çcountåå¹¶å°äžäžªcount matrixäžã
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- 1.è¿æ»€äœè¡šèŸŸçåºå
- 2.对衚蟟ç©éµè¿è¡normalization
- 3.çšè®¡ç®æ¹æ³å»é€batch effect
- 4.éè¿æ°æ®å¯è§åïŒåæé¢å€çæ æ²¡æèŸŸå°é¢æçææ
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- long RNA
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- 1.Peak Calling inside the long RNAs: æäº small RNA readsæ¥æºäºé¿RNAïŒåŠmRNAïŒlncRNAïŒççæ®µïŒlong RNA derived fragmentsïŒãè¿äºfragmentså¯èœå€æ°æ¥æºäºäžäºé¿RNAåšè¡æµäžæ¯èŸçš³å®çïŒäžå®¹æè¢«éè§£çå±éšåºåãæä»¬å¯ä»¥çšè®¡ç®æ¹æ³(åŠpeak callingç)å®ä¹åºè¿äºåºåïŒåéæ©æ§ç»è®¡è¿äºåºå(èéå šé¿èœ¬åœæ¬)çreadsæ°é(åšåé¢çæµçšåŸäžæä»¬å°å ¶ç§°äžº"domain features")ãè¿ç§åæ³äžæ¹é¢åšçç©åŠäžçžå¯¹æŽå åçïŒåŠäžæ¹é¢ä¹æåžæåå°åªå£°ç圱åïŒæé«åç±»ææãåš Help éšåïŒæä»¬äŒå¯¹å ·äœåæ³ç»åºæŽè¯Šç»ç诎æãå·²æç ç©¶è 对æ€è¿è¡äºäžäºç ç©¶ïŒè¯·å€§å®¶åèïŒ
- 2020 elife - Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling (2020, eLife, Jun Yao et al.)
- 2.Peak Calling in the unannotated regions: è¿æäº readsæ¥æºäºäžäºè¿å»æ²¡ææ³šéçåºåïŒæ¯åŠä¹åçäžç¯ç ç©¶åäºäºäžäºæ°ç RNAïŒç§°äžº oncRNA (orphan noncoding RNA)ãçžå ³æç« ïŒ
- 2018 Nature Medicine - Cancer cells exploit an orphan RNA to drive metastatic progression
- 2021 Gut - Unannotated small RNA clusters associated with circulating extracellular vesicles detect early stage liver cancer
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