Maser RNA-seq Genome Resequencing De novo Genome Sequencing Metagenome ChIP-seq CAGE BS-seq

Size: px

Start display at page:

Download "Maser RNA-seq Genome Resequencing De novo Genome Sequencing Metagenome ChIP-seq CAGE BS-seq"

ゆあかわらい
7 years ago
Views:

1 NGS Maser 2013/10/17

2 Maser RNA-seq Genome Resequencing De novo Genome Sequencing Metagenome ChIP-seq CAGE BS-seq

3 Maser RNA-seq Genome Resequencing De novo Genome Sequencing Metagenome ChIP-seq CAGE BS-seq

4 ( CLST) ( ) Maser

5 解析全体像のイメージ De novo Genome Sequencing バイオインフォマティシャン Genome Resequencing RNA-seq ChIP-seq Bisulfite-seq プログラミングスキルやツールマニュアルバイオDBの配列データや論文のMethod ノウハウ This image is modified from Nature Methods 6, S2 - S5 (2009) Photo is from morguefile 5

や論文のMethod ノウハウ This image is modified from Nature Methods 6, S2 - S5

6 解析全体像のイメージ De novo Genome Sequencing Genome Resequencing RNA-seq ChIP-seq Bisulfite-seq 配列データ This image is modified from Nature Methods 6, S2 - S5 (2009) Photo is from morguefile 6

modified from Nature Methods 6, S2 - S5 (2009) Photo is

7 : :

8 (1) (SRA) [](SRR) 2013/10 sra_stat.html

9 [] x WXS WGS (2) AMPLICON RNA-Seq ChIP-Seq CLONE Bisulfite-Seq DNase-Hyperse EST / FL-cDNA MeDIP-Seq / (SRA) ( )[](SRR) ( )[%] () (NGS) (): 2013/10 80% 60% 40% 20% 100% 0%

10 [] x WXS WGS AMPLICON RNA-Seq ChIP-Seq CLONE Bisulfite-Seq DNase-Hyperse EST / FL-cDNA MeDIP-Seq / RNA-Seq BS-seq ChIP-seq Genome Resequencing 300 CAGE De novo Genome Sequencing Metagenome

11 RNA-seq + de novo+ ( /) Fusion Bisulfite-seq CAGE Metagenome 16s rrna ChIP-seq ChIP-Seq QC Genome Resequencing SNV, InDel 1000 CNV/ De novo Genome Sequencing

12 Maser RNA-seq Genome Resequencing De novo Genome Sequencing Metagenome ChIP-seq CAGE BS-seq

13 (1) Maser () () Push Push

14 (2) Maser () ()

15 (3) Maser () ()

16 (4) Maser () ()

17 (5) Maser () ()

18 (6) Maser () ()

19 (7) Maser () ()

20 ( ) Data from ENCODE project MCF-7_cell_longPolyA(SRX084666), GM12878_cell_longPolyA(SRX082565), K562_cell_longPolyA(SRX084683)

21 Maser RNA-seq Genome Resequencing De novo Genome Sequencing Metagenome ChIP-seq CAGE BS-seq

22 RNA-Seq RNA-Seq 2 () ( )

23 RNA-Seq De novo Trinity-bowtie- express

24 UCSC Genome Browser Genome Explorer Genome Explorer RNA-seq Data is from Nature Mar 3;471(7336):68-73 ADS-iPSC(SRR094759) ADS(SRR094669) Sample A Data is from Nature Mar 3;471(7336):68-73 ADS-iPSC(SRR094759) ADS(SRR094669) () Sample B () Sample A () () Sample B () ()

25 A (Fastq) TopHat-Cufflinks (TopHat) A (BAM) (Cufflinks) A (GTF) B (Fastq) (TopHat) B (BAM) (Cufflinks) B (GTF) A (GTF) (Cuffdiff) (cuffdiff output) B (GTF) (Cuffmerge) (GTF) Nat Protoc Mar 1;7(3):562-78

26 TopHat-Cufflinks (1) 8 SampleA Splicing junction SampleA 2 SampleB Data is from Nature Mar 3;471(7336):68-73 ADS-iPSC(SRR094759) ADS(SRR094669) SampleB SambleA B 3 9

27 Cuffdiff Cuffdiff Data is from Nature Mar 3;471(7336):68-73 ADS-iPSC(SRR094759) ADS(SRR094669) Cuffdiff Isoform

28 Trinity-Bowtie-eXpress (Fasta) (Blast) (tsv) A (Fastq) (Bowtie) A (BAM) (express) B (Fastq) (Bowtie) B (BAM) A B A B

29 Trinity-Bowtie-eXpress Revigo GO Data from Array Express ERR HCT20152 thyroid ERR HCT20142 kidney ERR HCT20149 leukocyte ERR HCT20150 ovary ERR HCT20143 heart + Contig ID A B GO

30 Maser RNA-seq Genome Resequencing De novo Genome Sequencing Metagenome ChIP-seq CAGE BS-seq

31 ChIP-Seq DNA (IP) DNA Input DNA IP DNA IP

32 ChIP ChIP QC ENCODE QC (Fastq) (Bowtie) (BAM) ChIP-QC (phantompeakqualtools) (MACS) (html) (BED) (html)

33 (Fastq) ChIP (Bowtie) (BAM) (MACS) (BED) (html) IP IP This image is modified from the Nat Rev Genet Oct;10(10): Data of Genome Browser view on the right figures ChIP-Seq data from ENCODE project FOXA1_GSM (exp=SL2666,input=SL2665), GSM (input=SL2665) Input Input MACS2

34 (Fastq) (Bowtie) (BAM) (MACS) (BED) (html) (GADEM) DB (JASPAR) (MotIV)

35 ChIP-Seq Bowtie MACS Motif finding (Fastq) (Fastq) (Csfasta +qual) Bowtie1/2 BWA TMAP Bowtie (colorspace) (BAM) MACS PeakSeq SISSRs ZINBA SICER (BED) Motif finding

36 Maser RNA-seq Genome Resequencing De novo Genome Sequencing Metagenome ChIP-seq CAGE BS-seq

37 BS-seq(Bisulfite-seq) (Cm) Bisulfite() (C) (T) DNA m m m m Bisulfite m m m m 75% 25%

38 A:iPS(ADS-iPSC) B: (ADS) CpG (GenomeExplorer) 1 A B G C Data is from Nature Mar 3;471(7336):68-73 ADS(SRX026833) ADS-iPSC(SRX026835)

39 Bisulfite-Seq CG/CHG/CHH (50x) PBATBMap BMap A (Fastq) B (Fastq) (BMap) or (Bismark) (BMap) or (Bismark) A () B () ( ) ( ) A B () i.e)cpg,, bin, () (FET)

40 CpGID

41 GenomeExplorer C CG A B

42 Maser RNA-seq Genome Resequencing De novo Genome Sequencing Metagenome ChIP-seq CAGE BS-seq

43 Genome Resequencing SNV, INDEL (CNV) (SV) Nature Genetics 43, (2011) doi: /ng.806

44 Genome Resequencing BWA, GATK and snpeff + GE (Fastq) (BWA) (BAM) (GATK) (VCF) (snpeff + ) (TSV) SNV, INDEL 1000 PolyPhen2, PROVEAN

45 BWA, GATK and snpeff + GE

46 BWA, GATK and snpeff + GE (Fastq) (BWA) (BAM) (GATK) (VCF) (snpeff + ) (TSV) b / ID2 c / ID2 d / ID4 e / ID4 f / ID5 g / ID5 h / ID5 i / ID5 k / ID6 l / ID6 a / ID1 ID4 / ID3 j / ID6

47 (Fastq) (BWA) (BAM) (GATK) (VCF) (snpeff + ) (TSV) (Ins.) (Del.) (Ins.) (Del.)

48 (Fastq) (BWA) (BAM) (GATK) (VCF) (snpeff + ) (TSV) 1000 (%) PROVEAN (deleterious = ) PolyPhen2 (damaging = ) 0/0 0/1 1/1

49 (Fastq) (BWA) (BAM) (GATK) (VCF) (snpeff + ) (TXT) a / ID1 b / ID2 c / ID2 m / ID3 d / ID4 e / ID4 f / ID5 g / ID5 h / ID5 i / ID5 j / ID6 k / ID6 l / ID6

50 Maser RNA-seq Genome Resequencing De novo Genome Sequencing Metagenome ChIP-seq CAGE BS-seq

51 De novo Genome Sequencing ncrna

52 De novo Genome Sequencing annotation after assembling (Fastq) (Fasta) (Blast) (TSV) (JPEG) Illumina SOAPdenovo, Ray 454, IonPGM Newbler ( ) PacBio Sprai 100Mbase

53 annotation after assembling (Fastq) (Fasta) (Blast) (TSV) (JPEG)

54 K-mer (Fastq) (PNG) (Fasta) (ERX026224) (Blast) (TSV) (JPEG) K-mer 10 1, ,000 10,000, K-mer

55 (Fastq) (Fasta) (Blast) (TSV) (JPEG) Augustus Uniprot, NCBI NT Blast ( GC% ) Uniprot GO NCBI NT ()

56 (Fastq) (SRX026594) GC% (Fasta) (Blast) (TSV) (JPEG) () GC log10( )

57 PSMC (Fastq) (Fasta) (Blast) (TSV) (JPEG) ( ) Effective population size (x10 4 ) ~6 Heng Li, et al. Nature 475, (28 July 2011)

58 Maser RNA-seq Genome Resequencing De novo Genome Sequencing Metagenome ChIP-seq CAGE BS-seq

59 Metagenome DNA NGS 16S, 18S rrna Nature Sep 13;489(7415):250-6.

60 Metagenome blastn for NT database (Fastq) (Blast) Blast (TXT) (Megan) (TSV) 16S rdna SILVA Whole metagenome NCBI NT MEGAN (MEtaGenome ANalyzer) Daniel Huson

61 Metagenome (Fastq) (Blast) Blast (TXT) (Megan) Megan (TSV) SRR SRR SRR061704

62 Maser RNA-seq Genome Resequencing De novo Genome Sequencing Metagenome ChIP-seq CAGE BS-seq

63 CAGE 5 (TSS) mrna G 5

64 CAGE nant-icage IDR paraclu ver3.1 (Fastq) (BAM) (HTML) TSS (HTML) FANTOMCAGE IlluminaCAGE

65 (Fastq) ( ) ( ) (BAM) (HTML) TSS (HTML) A549 Gm12878 ( ) ( ) ( ) ( )

66 (Fastq) CAGE (BAM) (HTML) TSS (HTML) ()

67 (Fastq) (BAM) (HTML) TSS (HTML)

68 (Fastq) (BAM) (HTML) TSS (HTML)

69 CAGE

70 Maser RNA-seq Genome Resequencing De novo Genome Sequencing Metagenome ChIP-seq CAGE BS-seq

71 Maser

72 NGS

141025mishima

141025mishima NGS (RNAseq) »NGS Now Generation Sequencer»NGS»» 4 NGS(Next Generation Sequencer) Now Generation Sequencer http://www.youtube.com/watch?v=womkfikwlxm http://www.youtube.com/watch?v=mxkya9xcvbq http://www.youtube.com/watch?v=nhcj8ptycfc