第二代測(cè)序中數(shù)據(jù)分析轉(zhuǎn)錄組

組全組/外顯子SmallSNPSNPDenovoGenome轉(zhuǎn)錄組mRNAGene小RNAAnnotationandtargetTranscriptsSplicingsitesdiscoveryandGeneSNP/INDELAllelespecificGOandTrapnelletal.,AligntheRNA-seqreadstotheBowtieandAssembleexpressedgenesandCufflinksandIdentifydifferentiallyexpressedgenesandtranscriptExploredifferentialysisBowtie–SAM–TopHat –CummeRbund *Linux,64bitCPU,16GReadamntwithReadalignmentwith$Tophat-p8-Ggenes.gtf-oC1_R1_thoutgenomeC1_R1_1.fq$Tophat-p8-Ggenes.gtf-oC1_R2_thoutgenomeC1_R2_1.fq$Tophat-p8-Ggenes.gtf-oC1_R3_thoutgenomeC1_R3_1.fq$Tophat-p8-Ggenes.gtf-oC2_R1_thoutgenomeC2_R1_1.fq$Tophat-p8-Ggenes.gtf-oC2_R2_thoutgenomeC2_R2_1.fq$Tophat-p8-Ggenes.gtf-oC2_R3_thoutgenomeC2_R3_1.fqranscriptassemblywithranscriptassemblywithStep1$cufflinks-p8-oC1_R1_clout$cufflinks-p8-oC1_R2_clout$cufflinks-p8-oC1_R3_clout$cufflinks-p8-oC2_R1_clout$cufflinks-p8-oC2_R2_clout$cufflinks-p8-oC2_R3_cloutStep2:createafilecalledassemblies.txtthatliststheassemblyfileforeachsample.Step3:$cuffmerge-ggenes.gtf-sgenome.fa-p8ranscriptassemblywithCufflinksFPKMforFPKMfortranscript ysiswithDifferentialysiswith-uVisualizationwithLibrarycuff_data<-csScatter(gene(cuff_data),‘C1’,DownstreamdataFunctionannotation:GO,Mapman,Interpro,KEGG,Metacyc,etal.PathwaymapandProfilingFunctionenrienttestfordifferentialexpressedgenesetDownstream ysis:Loughlinet小RN