Data-analysis-and-management-of-high-throughput-sequencing-data

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1、DataAnalysis&Management!ofHigh-throughputSequencingData"QuoclinhNguyen"ResearchInformatics"GenomicsCore/MedicalResearchInstitute"CurrentIssues!CurrentIssues!The“QSEQ”file"Numberfilesperrun:120x8x(1

2、2)=960

3、1920filesNumberofreadsperrun:~40Mx8x(1

4、2)=~320M

5、640MTotaln

6、ucleotides(BPs):320Mx150x(1

7、2)=~48

8、96billionsWhatamIgoingtodowithmysequencingdata?"OverviewInfrastructure"So

9、!!Cufflinks!!MACS!Archives!RTA!VeryFastNASRTA!/!dragQandQdrop!Gigabit!netowrk!/rcgenomics(20TBs)NAS/SAN!400TBs!MySQL!Oracle!SSH,FTP!hRp://lims.csms.edu!VMServer(Linux)LAMP!SMB,HTTP!Analysis!/!Mining!!LIMS(NGS/Microarray)Linux!(VM!&!Physical)!"OverviewInfrastructure

10、"So

11、TBs!>300nodesX2CPU=>600CPUs>300nodesx4G=>1200GsFastNASstoragecapacity~100TBsOtherstoragedevices~400TBsRNA-SeqAnalysisPipeline!Phase&1:&NGS&data&processing&Phase&2:&Basic&Analysis&Phase&3:&Downstream&Analysis&&&&&input!Binary!Data!Sample!1!….!Sample!N!genes.expr

12、!transcripts.expr!BCL!files!BAM!BAM!hits.bam!transcripts.gif!Raw!Data!BAM!Q>!FASTQ!Cuffcompare!QSEQ!files!TopHat!Cuffdiff!Mapped!Reads!SAM!Q>BAM!!Mapped!reads!UCSC!!BAM!file!QCbysamtools!CLCBIO!Cufflinks!clean!genes/express!output!deliver!results!BAM!files!files!DataProc

13、essing!Phase&1:&NGS&data&processing&Binary!Data!BCL!files!QC/Datafiltering•Binandremoveindexes•Removeadapters(ifany)Raw!Data!•RemoveduplicateQSEQ!files!•Removalofnon-mappedsequences•FilteroutreadmappingtoribosomalRNA•Percentageofribosomal?Mapped!Reads!SAM!Q>BAM!!QS

14、EQfiles->Alignedfiles(BAM)QCbysamtools!•Parallelprocessing(MPI)•Whatisinthealignmentfiles?clean!BAM!files!The“BAM/SAM”file"BAM(BinaryAlignmentMapp