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11/06/2014 RNA Seq analysis Cleaning Plateforme ABiMS RNA Seq analysis : cleanning Data Cleaning Why do we care about cleaning ? Why do we care about cleaning ? RAW SEQUENCES Why do we care about cleaning ? RAW SEQUENCES AMAZING TRANSCRIPTOME !!! Why do we care about cleaning ? RAW SEQUENCES AMAZING TRANSCRIPTOME !!! NO !! Because… •  Unknown nucleoNdes •  Bad quality nucleoNdes •  Adaptors and primers sub-‐ sequences •  Poly A/T tails •  Low complexity sequences •  rRNA sequences •  Contaminant sequences •  Short length sequences But also: •  Removing singletons •  In-‐silico normalizaNon •  Sequencing errors correcNon •  … But ﬁrst… What data do we have ? NGS sequences •  Illumina, 454 (Roche), Ion Torrent, Solid, … •  Single, Paired-‐end, Mate pairs •  Sequences length: 25, 35, 50, 75, 100, 150, 250, 500, 700, 800, … base pairs •  File format: Fastq Phred+33, Fastq Phred+64, 2 ﬁles (.fasta + .qual), Colorspace

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11/06/2014. RNA Seq analysis. Cleaning. Plateforme ABiMS File format: Fastq Phred+33, Fastq Phred+64,. 2 files (.fasta + .qual), Colorspace

RNA Seq analysis PDF

102 Pages·2014·6.21 MB·English

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by Unknow| 2014| 102 pages| 6.21| English

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11/06/2014. RNA Seq analysis. Cleaning. Plateforme ABiMS File format: Fastq Phred+33, Fastq Phred+64,. 2 files (.fasta + .qual), Colorspace

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Author:	Unknown
Publication Year:	2014
Pages:	102
Language:	English
File Size:	6.21
Format:	PDF
Price:	FREE

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