Transcriptome Sequence
(NGS)   RNA-seq(         )    NGS
(NGS)    RNA-seq(                   )          genome DNA       mapping          mapping    NGS
RNA-seq mapping tools;Tuxedo toolsBowtie - http://bowtie.cbcb.umd.edu/ genome DNA         index            mappingTopHat -...
RNA-seqNGS       RNA-seq(              NCBI SRA   DL etc.)    bowtie index       reference genomeTopHat RNA-seq mappingTop...
NGS:   .fastq file                       (+ reference genome data)                     TopHat          .sam file            ...
# fastq              genome mapping# paired-end                          mate innner distance$ tophat -r 50 --solexa-quals...
.gtfCuffcompare:            annotation data(reference   gtf   ensembl                 )$ cuffcompare /path/to/reference/re...
cufflinks• reference                  transcript                      (refmap)• transcript                 reference gene  ...
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Transcriptome Sequenceによる遺伝子発現解析の実際

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AJACS19 & 第22回DDBJing 講習会 in 東京

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  • Transcriptome Sequenceによる遺伝子発現解析の実際

    1. 1. Transcriptome Sequence
    2. 2. (NGS) RNA-seq( ) NGS
    3. 3. (NGS) RNA-seq( ) genome DNA mapping mapping NGS
    4. 4. RNA-seq mapping tools;Tuxedo toolsBowtie - http://bowtie.cbcb.umd.edu/ genome DNA index mappingTopHat - http://tophat.cbcb.umd.edu/ RNA-seq mapping splice junctionCufflinks - http://cufflinks.cbcb.umd.edu/ mapping RNA-seq assemble
    5. 5. RNA-seqNGS RNA-seq( NCBI SRA DL etc.) bowtie index reference genomeTopHat RNA-seq mappingTopHat Cufflinkstranscriptome assemble( )
    6. 6. NGS: .fastq file (+ reference genome data) TopHat .sam file Cufflinks.gtf file assemble transcriptome
    7. 7. # fastq genome mapping# paired-end mate innner distance$ tophat -r 50 --solexa-quals /path/to/bowtie-indexes/chr1 /path/to/samples/exp_1.fq /path/to/samples/exp_2.fq# accepted_hits.sam# mate innner distance$ cufflinks -m 50 /path/to/exp_tophat_out/accepted_hits.sam
    8. 8. .gtfCuffcompare: annotation data(reference gtf ensembl )$ cuffcompare /path/to/reference/reference.gtf /path/to/cufflinks_output/transcript.gtf
    9. 9. cufflinks• reference transcript (refmap)• transcript reference gene (tmap) Cufflinks splicing junction Trapnell et al. (2010) nature biotechnology

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