[[Python¥Ð¥¤¥ª]]¡¡[[Python¥Ð¥¤¥ª/¥Ä¡¼¥ë]]~
&counter();¡¡¡¡¡¡&lastmod();~

*ʬÀϥġ¼¥ë [#e7c82741]

-[[Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation (Nature Biotechnology volume 28, pages 511–515 (2010)):https://www.nature.com/articles/nbt.1621]]
-[[Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms(PubMed):https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3146043/]]

-[[Third-generation sequencing fireworks at Marco Island (Nature Biotechnology volume 28, pages 426–428 (2010)):https://www.nature.com/articles/nbt0510-426]]

-[[Advancing RNA-Seq analysis (Nature Biotechnology volume 28, pages 421–423 (2010)):https://www.nature.com/articles/nbt0510-421]]

-[[RNA-Seq¤Î¿ôÍý¡½À¸À®¥â¥Ç¥ë¤Ë¤è¤ëȯ¸½ÎÌ¿äÄê¡§¥¢¡¼¥«¥¤¥Ö - Wolfeyes Bioinformatics beta:http://yagays.github.io/blog/2013/07/14/mathematical-models-for-transcriptome-quantification-0/]]

-[[Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334321/pdf/nihms-366741.pdf]]


-[[BaseSpace ¤Ç¹Ô¤¦ RNA-seq ÆþÌç¡¡< TopHat/CufflinksÊÔ> 2015_ilmn_webinar_basespace-rna_session12.pdf:https://jp.illumina.com/content/dam/illumina-marketing/apac/japan/documents/pdf/2015_ilmn_webinar_basespace-rna_session12.pdf]]

-[[RNA-Seq¡Ã¼¡À¤Â奷¡¼¥±¥ó¥µ¡¼¡¡¤ªÇº¤ß¥«¥¦¥ó¥»¥ê¥ó¥°(2013):http://www.mss.co.jp/businessfield/bioinformatics/ngs/pop_rna-seq.html]]

-[[(ERANGE) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Method 2008:https://www.ncbi.nlm.nih.gov/pubmed/18516045]]
-[[(ERANGE) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Method 2008 (ResearchGate copy):https://www.researchgate.net/publication/5331349_Mapping_and_quantifying_mammalian_transcriptomes_by_RNA-Seq/download]]


------------------------

**Cuffdiff (Cufflinks) [#sb90c59c]

cufflinks¤Ç¥¨¥é¡¼¤¬½Ð¤ë¡£[[HISAT2-StringTie-Cuffdiff error: BAM record error: found spliced alignment without XS attribute:https://www.biostars.org/p/222849/]]¡ÊÀµ¤·¤¯¤Ï¡©¡Ë

Âкö¤Ï¡¢HISAT2¤Ç¥Ñ¥é¥á¡¼¥¿--dta-cufflinks¤ò»ØÄꤹ¤ë¤³¤È
 
***cufflinks/cuffdiff [#ed355856]
-[[cufflinks:https://github.com/cole-trapnell-lab/cufflinks]]
^[[Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks:https://www.nature.com/articles/nprot.2012.016]]
-[[binary download page:http://cole-trapnell-lab.github.io/cufflinks/install/]]

cuffdiff¤ò»È¤Ã¤Æ¤ß¤ë
cuffdiff¤ò»È¤Ã¤Æ¤ß¤ë 2019-06-29 ºÆÅÙ¤ä¤êľ¤¹É¬Íפ¢¤ê¤½¤¦¡£¤Þ¤ºcufflinks¤Ç½¸·×¤¬É¬Íפ«¤â¡£Í×¥Á¥§¥Ã¥¯¡£

-[[Cufflinks | RNA-seq ¤òÍøÍѤ·¤¿°äÅÁ»Òȯ¸½²òÀÏ:https://bi.biopapyrus.jp/rnaseq/expression/cufflinks.html]]

¤¢¤é¤«¤¸¤áÍѰդ·¤¿sortºÑ¤ß¤Îbam¥Õ¥¡¥¤¥ëSRR4535xx.tagged.sorted.bam ¤È¥Þ¥Ã¥×s288c_3.gff¤ËÂФ·¤Æ
 $cuffdiff -p 32 -o ./results1 ../s288c_e.gff -L batch,chemo \
 SRR453566.tagged.sorted.bam,SRR453567.tagged.sorted.bam,SRR453568.tagged.sorted.bam \
 SRR453569.tagged.sorted.bam,SRR453570.tagged.sorted.bam,SRR453571.tagged.sorted.bam
¥é¥Ù¥ëÉÕ¤±-L¤ÎÅÔ¹ç¤Ç¡¢¥é¥Ù¥ë£²¼ïÎàbatch,chemo¤ËÂФ·¤Æ¡¢ÆþÎÏ¥Õ¥¡¥¤¥ëSRR453566,67,68¤òbatch¤Ë¡¢SRR453569,70,71¤òchemo¤Ë³ä¤êÅö¤Æ¤¿¡Ê¤Ï¤º¡Ë¡£¥³¥ó¥Þ¤ÎÁ°¸å¤Ï¶õÇò¤Ê¤·¡Ê¤¢¤ë¤È¥³¥Þ¥ó¥É²ò¼á¤Ç°ú¿ô¤ÎÀÚ¤ìÌܤȻפäƤ·¤Þ¤¦¤Î¤Ç¡Ë¡¡¤³¤Î-L¤ÈÆþÎÏ¥Õ¥¡¥¤¥ë¤Î¶èÀÚ¤ê¤Ë¤è¤Ã¤Æ¡¢¸å¤Î²òÀϥѥ¿¡¼¥ó¡Ê¥½¡¼¥¹¤ÎʬÎà¡Ë¤¬·è¤Þ¤ë¤Î¤ÇÍ×Ãí°Õ¡£

 Warning: Could not connect to update server to verify current version. Please check
   at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
 [10:38:24] Loading reference annotation.
 [10:38:25] Inspecting maps and determining fragment length distributions.
 [10:40:50] Modeling fragment count overdispersion.
 [10:42:08] Modeling fragment count overdispersion.
 > Map Properties:
 >	Normalized Map Mass: 3618635.35
 >	Raw Map Mass: 3746966.57
 >	Fragment Length Distribution: Empirical (learned)
 >	              Estimated Mean: 209.34
 >	           Estimated Std Dev: 99.53
 > Map Properties:
 >	Normalized Map Mass: 3618635.35
 >	Raw Map Mass: 5136465.50
 >	Fragment Length Distribution: Empirical (learned)
 >	              Estimated Mean: 213.53
 >	           Estimated Std Dev: 96.07
 > Map Properties:
 >	Normalized Map Mass: 3618635.35
 >	Raw Map Mass: 3780062.80
 >	Fragment Length Distribution: Empirical (learned)
 >	              Estimated Mean: 206.94
 >	           Estimated Std Dev: 94.02
 > Map Properties:
 >	Normalized Map Mass: 3618635.35
 >	Raw Map Mass: 2502112.93
 >	Fragment Length Distribution: Empirical (learned)
 >	              Estimated Mean: 202.52
 >	           Estimated Std Dev: 96.05
 > Map Properties:
 >	Normalized Map Mass: 3618635.35
 >	Raw Map Mass: 3127907.67
 >	Fragment Length Distribution: Empirical (learned)
 >	              Estimated Mean: 211.12
 >	           Estimated Std Dev: 94.18
 > Map Properties:
 >	Normalized Map Mass: 3618635.35
 >	Raw Map Mass: 3898613.50
 >	Fragment Length Distribution: Empirical (learned)
 >	              Estimated Mean: 213.42
 >	           Estimated Std Dev: 98.72
 [10:43:25] Calculating preliminary abundance estimates
 [10:43:25] Testing for differential expression and regulation in locus.
 > Processed 6278 loci.                         [*************************] 100%
 Performed 5732 isoform-level transcription difference tests
 Performed 0 tss-level transcription difference tests
 Performed 5732 gene-level transcription difference tests
 Performed 0 CDS-level transcription difference tests
 Performed 0 splicing tests
 Performed 0 promoter preference tests
 Performing 0 relative CDS output tests
 Writing isoform-level FPKM tracking
 Writing TSS group-level FPKM tracking
 Writing gene-level FPKM tracking
 Writing CDS-level FPKM tracking
 Writing isoform-level count tracking
 Writing TSS group-level count tracking
 Writing gene-level count tracking
 Writing CDS-level count tracking
 Writing isoform-level read group tracking
 Writing TSS group-level read group tracking
 Writing gene-level read group tracking
 Writing CDS-level read group tracking
 Writing read group info
 Writing run info

 $ cd results1
 $ ls
 bias_params.info         cds_exp.diff          genes.read_group_tracking     promoters.diff      tss_groups.count_tracking
 cds.count_tracking       cuffData.db           isoform_exp.diff              read_groups.info    tss_groups.fpkm_tracking
 cds.diff                 gene_exp.diff         isoforms.count_tracking       run.info            tss_groups.read_group_tracking
 cds.fpkm_tracking        genes.count_tracking  isoforms.fpkm_tracking        splicing.diff       var_model.info
 cds.read_group_tracking  genes.fpkm_tracking   isoforms.read_group_tracking  tss_group_exp.diff

¤³¤ÎÎã¤Ç¤Ï¡ÊCDS¤¬½ñ¤¤¤Æ¤¤¤Ê¤¤¤Î¤Ç¡©¡Ëgene_exp.diff¤Èisoforms_exp.diff¤¬·ë²Ì¤Ë¤Ê¤Ã¤Æ¤¤¤ë¡£

gene_exp.diff¤ò¸«¤ë¤È
#ref(SRR453566-cuffdiff-gene-exp-diff.png);

isoforms_exp.diff¤ò¸«¤ë¤È
#ref(SRR453566-cuffdiff-isoforms-exp-diff.png);

¸µÏÀʸ~
[[Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks (Nat Protoc. ; 7(3): 562&#8211;578):https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334321/pdf/nihms-366741.pdf]]~
¤Ë¤è¤ë¤È¡¢¤³¤Î·ë²Ì¤Ï[[cummeRbund:https://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html]]¤Ë¤è¤Ã¤Æ²Ä»ë²½¤Ç¤­¤ë¡£~
¼ê½ç¤Ï¤¿¤È¤¨¤Ð
--[[CummeRbund¤Ç°äÅÁ»Òȯ¸½¤Î¥×¥í¥Ã¥È¤ò°äÅÁ»Ò¤´¤È¤Ëʤ٤ë - Qiita:https://qiita.com/yuifu/items/cc9730f7e3a1277f6c50]]
--[[cummeRbund-example-workflow.pdf:https://www.bioconductor.org/packages/release/bioc/vignettes/cummeRbund/inst/doc/cummeRbund-example-workflow.pdf]]¡¡¸åȾ¤¬Ì¤´°À®¤ÇÅÓÃæ¤Þ¤Ç¤·¤«¤Ê¤¤¡ª¡ª
--[[cummeRbund-manual.pdf:https://www.bioconductor.org/packages/release/bioc/vignettes/cummeRbund/inst/doc/cummeRbund-manual.pdf]]¡¡¥Þ¥Ë¥å¥¢¥ëÉ÷¤À¤¬¼ê½ç¤â¿¾¯°Õ¼±¤·¤Æ¤¤¤ë¡©

**cummeRbund¤ò»È¤¦ [#c8ee86ea]
-[[Bioconductor - cummeRbund::https://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html]]
-[[CummeRbund: Visualization and Exploration of Cufflinks High-throughput Sequencing Data:https://www.bioconductor.org/packages/release/bioc/vignettes/cummeRbund/inst/doc/cummeRbund-manual.pdf]]¡¡¤³¤³¤Ë½Ð¤Æ¤¤¤ë¥×¥í¥»¥¹¤Ë½¾¤Ã¤Æ°Ê²¼¼Â¸³¤¹¤ë¡£
-[[cummeRbund Example Workflow:https://www.bioconductor.org/packages/release/bioc/vignettes/cummeRbund/inst/doc/cummeRbund-example-workflow.pdf]]¡¡¤³¤ì¤Ï½ñ¤­¤«¤±¤Î¾õÂ֤Τ褦¤Ç¡¢¸åȾ¤¬¶õÇò¡£
-[[¥ê¥Õ¥¡¥ì¥ó¥¹¥Þ¥Ë¥å¥¢¥ë:https://www.bioconductor.org/packages/release/bioc/manuals/cummeRbund/man/cummeRbund.pdf]]


cummeRbund¤ÎÆþÎϤÏcuffDiff¤Î·ë²Ì¤Ç¡¢cummeRband¤Ç¤Î²òÀϤΤ¿¤á¤ËcuffDiff¤Ç¥é¥Ù¥ëÉÕ¤±¤ò¤·¤Æ¤¢¤ë¤³¤È¡£¤½¤Î¥é¥Ù¥ë¤ò¸µ¤Ë¡¢Èæ³Ó¤ò¼è¤Ã¤¿¤ê¤¹¤ë¡£

 ¥Ç¡¼¥¿¥ë¡¼¥È
    SRR453566.tagged.sorted.bam
    SRR453567.tagged.sorted.bam
    ...
    SRR453571.tagged.sorted.bam
    results1
        bias_params.info
        cds_exp.diff
        genes.read_group_tracking
        promoters.diff
        tss_groups.count_tracking
        cds.count_tracking
        isoform_exp.diff
        read_groups.info
        tss_groups.fpkm_tracking
        cds.diff
        gene_exp.diff
        isoforms.count_tracking
        run.info
        tss_groups.read_group_tracking
        cds.fpkm_tracking
        genes.count_tracking
        isoforms.fpkm_tracking
        splicing.diff
        var_model.info
        cds.read_group_tracking
        genes.fpkm_tracking
        isoforms.read_group_tracking
        tss_group_exp.diff
  ¢¬  ¤³¤Î¥ì¥Ù¥ë¤òR¤Î¥ï¡¼¥­¥ó¥°¥Ç¥£¥ì¥¯¥È¥ê¤Ë¤·¤Æ¤ª¤¯¡£

R¤òµ¯Æ°¡£
 > library(cummeRbund)    ¥×¥í¥°¥é¥àcummRbund¤ò¥í¡¼¥É
 > cuff<-readCufflinks("results1")  ¥Ç¥£¥ì¥¯¥È¥ê results1 ¤«¤é¥Ç¡¼¥¿ÆÉ¹þ¤ó¤Ç¥Ç¡¼¥¿¥Ù¡¼¥¹¤Ë½ñ¤­¹þ¤à
 (Ãí) > cuff <- readCufflinks('results1', gtfFile='../s288c_e.gff')¤Ïgenome=¤¬Ìµ¤¤¤È¥À¥á¡£genome=¤Ë½ñ¤±¤ëÃͤ¬ÉÔÌÀ
   A character string indicating to which genome build the .gtf annotations belong
   (e.g. ¡Çhg19¡Ç or ¡Çmm9¡Ç)
 > cuff
 CuffSet instance with:
 	 2 samples
 	 6445 genes
 	 6445 isoforms
 	 0 TSS
 	 0 CDS
 	 0 promoters
 	 0 splicing
 	 0 relCDS
 > disp<-dispersionPlot(genes(cuff))
 > disp
 > dens<-csDensity(genes(cuff))
 > dens
 > b<-csBoxplot(genes(cuff))
 > b
 > sm<-csScatterMatrix(genes(cuff))
 > sm
 > s<-csScatter(genes(cuff),"chemo","batch",smooth=T)
  chemo¤Èbatch¤Ç¤Î»¶ÉÛ¿Þ
 > s
 > dend<-csDendro(genes(cuff)) 
 > dend
 > m<-MAplot(genes(cuff),"chemo","batch")
 > m
 > v<-csVolcanoMatrix(genes(cuff))
 > v
 > mySigGeneIds<-getSig(cuff,alpha=0.05,level='genes')
 > lengthh(mySigGeneIds)
 > sigGenes<-getGenes(cuff,sigGeneIds)
 sigGenes
 CuffGeneSet instance for  3900  genes
  
 Slots:
 	 annotation
 	 fpkm
 	 repFpkm
 	 diff
 	 count
 	 isoforms	 CuffFeatureSet instance of size 3900 
 	 TSS		 CuffFeatureSet instance of size 0 
 	 CDS		 CuffFeatureSet instance of size 0 
 	 promoters		 CuffFeatureSet instance of size 3900 
 	 splicing		 CuffFeatureSet instance of size 0 
 	 relCDS		 CuffFeatureSet instance of size 3900 
 > head(annotation(genes(cuff)))
     gene_id class_code nearest_ref_id gene_short_name
 1 gene_0001       <NA>           <NA>            PAU8
 2 gene_0002       <NA>           <NA>       YAL067W-A
 3 gene_0003       <NA>           <NA>            SEO1
 4 gene_0004       <NA>           <NA>         YAL065C
 5 gene_0005       <NA>           <NA>       YAL064W-B
 6 gene_0006       <NA>           <NA>            TDA8
                     locus length coverage feature_id isoform_id seqnames
 1   NC_001133.9:1806-2169     NA       NA         NA       <NA>     <NA>
 2   NC_001133.9:2479-2707     NA       NA         NA       <NA>     <NA>
 3   NC_001133.9:7234-9016     NA       NA         NA       <NA>     <NA>
 4 NC_001133.9:11564-11951     NA       NA         NA       <NA>     <NA>
 5 NC_001133.9:12045-12426     NA       NA         NA       <NA>     <NA>
 6 NC_001133.9:13362-13743     NA       NA         NA       <NA>     <NA>
   source type start end score strand frame
 1   <NA>   NA    NA  NA    NA   <NA>  <NA>
 2   <NA>   NA    NA  NA    NA   <NA>  <NA>
 3   <NA>   NA    NA  NA    NA   <NA>  <NA>
 4   <NA>   NA    NA  NA    NA   <NA>  <NA>
 5   <NA>   NA    NA  NA    NA   <NA>  <NA>
 6   <NA>   NA    NA  NA    NA   <NA>  <NA>
 > head(fpkm(genes(cuff)))
 > head(count(genes(cuff)))
 > head(fpkm(isoforms(cuff)))
 > head(diffData(genes(cuff)))
 > head(fpkmMatrix(genes(cuff)))

¶½Ì£¤¢¤ëgene(½¸¹ç)¤ò»ØÄꤷ¤ÆÊ¬ÀϤ¹¤ë
 > myGeneIds <- c("gene_0010", "gene_0010", "gene_0011", "gene_0012", "gene_0013", "gene_0014", "gene_0015", "gene_0016", "gene_0017", "gene_0018", "gene_0019")
   ¶½Ì£¤Î¤¢¤ëgeneid¤ò¥ê¥¹¥È¤·¤¿¤â¤Î¡£¤¢¤é¤«¤¸¤áºî¤Ã¤Æ¤¢¤ë¤È¤¹¤ë¡£¤³¤³¤Ï²¾¤ÎÎã¡£
 > myGenes <- getGenes(cuff,myGeneIds)
 > myGenes
 CuffGeneSet instance for  10  genes
  
 Slots:
 	 annotation
 	 fpkm
 	 repFpkm
 	 diff
 	 count
 	 isoforms	 CuffFeatureSet instance of size 10 
 	 TSS		 CuffFeatureSet instance of size 0 
 	 CDS		 CuffFeatureSet instance of size 0 
 	 promoters		 CuffFeatureSet instance of size 10 
 	 splicing		 CuffFeatureSet instance of size 0 
 	 relCDS		 CuffFeatureSet instance of size 10 
 > myGeneset.pluri<-getGenes(cuff,myGeneIds,sampleIdList=c("batch"))
 > h<-csHeatmap(myGenes,cluster='both')
 > h
 > b<-expressionBarplot(myGenes)
 > b
 > s<-csScatter(myGenes,"chemo","batch",smooth=T)
 > s
 > v<-csVolcano(myGenes,"chemo","batch")
 > v
 > ih<-csHeatmap(isoforms(myGenes),cluster='both',labRow=F)
 > ih
 > th<-csHeatmap(TSS(myGenes),cluster='both',labRow=F)
 > th
 > den<-csDendro(myGenes)
 > den

£±¤Ä¤À¤±¤Ë¤¹¤ë
 > myGeneId <- c("gene_0010")        1¤Ä¤À¤±¤Ë¤¹¤ë
 > myGene<-getGene(cuff,myGeneId)
 > head(fpkm(myGene))       Ʊ¤¸¤è¤¦¤Ë»È¤¨¤ë
 > gl<-expressionPlot(myGene)
 > gl
 > gl.iso.rep<-expressionPlot(isoforms(myGene),replicates=T)
 > gb<-expressionBarplot(myGene)
 > gb
 > igb<-expressionBarplot(isoforms(myGene),replicates=T)
 > gp<-csPie(myGene,level="isoforms")
 > gp


 > mySigMat<-sigMatrix(cuff,level='genes',alpha=0.05)
 > mySigMat
 > mySigGeneIds<-getSig(cuff,alpha=0.05,level='genes')
 > head(mySigGeneIds)
 > chemo_vs_batch.sigIsoformIds<-getSig(cuff,x='chemo',y='batch',alpha=0.05,level='isoforms')


 > myDistHeat<-csDistHeat(genes(cuff))
 > myDistHeat
 > myRepDistHeat<-csDistHeat(genes(cuff),replicates=T)
 > myRepDistHeat
 > genes.PCA<-PCAplot(genes(cuff),"PC1","PC2")
 > genes.PCA
 > genes.MDS<-MDSplot(genes(cuff))
  cmdscale(d, eig = TRUE, k = 2) ¤Ç¥¨¥é¡¼: 
   'k' must be in {1, 2, ..  n - 1}    MDS(multi-dimensional scaling)¤Ï¼¡¸µ¿ô3°Ê¾å

¥¯¥é¥¹¥¿²½
 > ic<-csCluster(myGenes,k=4)
 > ic
 > ic$cluster
 gene_0010 gene_0011 gene_0013 gene_0014 gene_0015 gene_0016 gene_0017 
         1         1         2         2         3         3         4 
 gene_0018 gene_0019 
         3         3 
 > icp<-csClusterPlot(ic)
 > icp

Îà»÷gene¤Î¸¡½Ð
 > mySimilar<-findSimilar(cuff,myGeneId,n=20)
 > mySimilar.expression<-expressionPlot(mySimilar,logMode=T,showErrorbars=F)
 > mySimilar.expression
 
 > myProfile<-c(500,0,400)
 > mySimilar2<-findSimilar(cuff,myProfile,n=10)
 > mySimilar2.expression<-expressionPlot(mySimilar2,logMode=T,showErrorbars=F)
 > mySimilar2.expression

 > head(annotation(genes(cuff)))
     gene_id class_code nearest_ref_id gene_short_name
 1 gene_0001       <NA>           <NA>            PAU8
 2 gene_0002       <NA>           <NA>       YAL067W-A
 3 gene_0003       <NA>           <NA>            SEO1
 4 gene_0004       <NA>           <NA>         YAL065C
 5 gene_0005       <NA>           <NA>       YAL064W-B
 6 gene_0006       <NA>           <NA>            TDA8
                     locus length coverage feature_id isoform_id seqnames
 1   NC_001133.9:1806-2169     NA       NA         NA       <NA>     <NA>
 2   NC_001133.9:2479-2707     NA       NA         NA       <NA>     <NA>
 3   NC_001133.9:7234-9016     NA       NA         NA       <NA>     <NA>
 4 NC_001133.9:11564-11951     NA       NA         NA       <NA>     <NA>
 5 NC_001133.9:12045-12426     NA       NA         NA       <NA>     <NA>
 6 NC_001133.9:13362-13743     NA       NA         NA       <NA>     <NA>
   source type start end score strand frame
 1   <NA>   NA    NA  NA    NA   <NA>  <NA>
 2   <NA>   NA    NA  NA    NA   <NA>  <NA>
 3   <NA>   NA    NA  NA    NA   <NA>  <NA>
 4   <NA>   NA    NA  NA    NA   <NA>  <NA>
 5   <NA>   NA    NA  NA    NA   <NA>  <NA>
 6   <NA>   NA    NA  NA    NA   <NA>  <NA>




¡Á¡Á¡Á¡Á¡Á¡Á¡Á¡Á¡Á
**¤â¤¦°ìÅÙÊÙ¶¯ [#y2c99830]
¤½¤ÎÁ°¤Ë
-NIG¤Î¥Ñ¥¤¥×¥é¥¤¥ó¥µ¡¼¥Ó¥¹¡¡[[NGS¥¢¥×¥ê¥±¡¼¥·¥ç¥ó Pipline-Menu-wiki:http://cell-innovation.nig.ac.jp/maser/Applications/applications_top.html]]¡¢¡¡[[Äó¶¡Á´¥Ñ¥¤¥×¥é¥¤¥ó¥ê¥¹¥È All-Pipelines:http://cell-innovation.nig.ac.jp/maser_cgi/cip-pl_list_violin_ja.cgi]]¡¢¤È¡¡[[RNA-seq¤Î¥Ñ¥¤¥×¥é¥¤¥ó:http://cell-innovation.nig.ac.jp/maser/Applications/RNA-seq.html]]

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-¼ç¡¡[[Tuxedo Genome Guided Transcriptome Assembly Workshop &#183; trinityrnaseq/RNASeq_Trinity_Tuxedo_Workshop Wiki:https://github.com/trinityrnaseq/RNASeq_Trinity_Tuxedo_Workshop/wiki/Tuxedo-Genome-Guided-Transcriptome-Assembly-Workshop]]
-ÄɲÃ
--[[RNA seq ¶¤Î£² ¥Þ¥Ã¥Ô¥ó¥°¤«¤éÅý·×½èÍý¤Þ¤Ç - mac¤Ç¥¤¥ó¥Õ¥©¥Þ¥Æ¥£¥¯¥¹:http://kazumaxneo.hatenablog.com/entry/2017/03/27/141521]]~
--[[RNA seq ¶¤Î£³ ¥Ò¡¼¥È¥Þ¥Ã¥×ºîÀ® - mac¤Ç¥¤¥ó¥Õ¥©¥Þ¥Æ¥£¥¯¥¹:http://kazumaxneo.hatenablog.com/entry/2017/03/29/171543]]
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-¤ª¤Þ¤±
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--Ãæ²¬¿µ¼£ [[°äÅÁ»Òȯ¸½²òÀÏÆþÌç:http://coop-math.ism.ac.jp/files/216/%E8%B3%87%E6%96%99_nakaoka.pdf]]¡¡¥¹¥é¥¤¥É13°Ê¹ß¤¬RNA-seq ¾¯¤·¸Å¤¤¤«¡©
--¥¢¥á¥ê¥¨¥Õ¡¡R N A - s e q [[20150805and28_yamaguchi.pdf https://biosciencedbc.jp/gadget/human/20150805and28_yamaguchi.pdf]]

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