Exome Project - Revision history

Christoph: /* See also */

2012-07-17T21:46:45Z

‎See also

2012-07-17T21:07:34Z

‎See also

2012-07-17T21:00:13Z

‎See also

2012-07-17T20:02:53Z

2012-07-17T01:02:23Z

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2012-07-17T00:01:36Z

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2012-07-16T21:59:01Z

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2012-07-16T21:54:20Z

‎Glossary

2012-07-16T21:29:12Z

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2012-07-16T21:19:06Z

‎Glossary

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 *[http://genome.ucsc.edu/FAQ/FAQformat.html UCSC Data File Formats FAQ]
 *[http://biopython.org/wiki/Multiple_Alignment_Format Multiple Alignment Format] @Biopython
 ==References==

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 *[[FASTQ format]]
 *[http://genome.ucsc.edu/FAQ/FAQformat.html UCSC Data File Formats FAQ]
 ==References==

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 *[[wikipedia:Non allelic homologous recombination]]
 *[[FASTQ format]]
 ==References==

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 :;mappedReads : the sum of all the numbers in the column with header Total gene reads. The Total gene reads for a gene is the total number of reads that after mapping have been mapped to the region of the gene. Thus this includes all the reads uniquely mapped to the region of the gene as well as those of the reads which match in more places that have been allocated to this gene's region. A gene's region is that comprised of the flanking regions (if it was specified in figure 18.127), the exons, the introns and across exon-exon boundaries of all transcripts annotated for the gene. Thus, the sum of the total gene reads numbers is the number of mapped reads for the sample.
 :;exonLength : the number in the column with the header Exon length in the row for the gene, divided by 1000. This is calculated as the sum of the lengths of all exons annotated for the gene. Each exon is included only once in this sum, even if it is present in more annotated transcripts for the gene. Partly overlapping exons will count with their full length, even though they share the same region.
 ==See also==

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 *whole genome assembly comparison (WGAC) and whole genome shotgun sequence detection (WSSD)
 *[[wikipedia:Non allelic homologous recombination]]
 ==References==

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 *[[wikipedia:Array-comparative genomic hybridization]] (array CGH)
 *[[wikipedia:Fisher's exact test]]
 ==References==

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 *[[wikipedia:Missense mutation]]
 *minor allele frequency (MAF)
 *[[wikipedia:Fisher's exact test]]

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 ;monogenic : simple and rare diseases
 ;multigenic : complex and common diseases
 ;RPKM : Reads Per Kilobase of exon model per Million mapped reads. Defined as:<ref>Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL, Zhao

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 *[[wikipedia:Exome sequencing]]
 *[[wikipedia:Genome-wide association studies]] (GWASs)
-*[[wikipedia:Copy-number variation]]
+*[[wikipedia:Copy-number variation]] (CNV)
 *[[wikipedia:International HapMap Project]]
 *homozygosity mapping

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 ;RPKM : Reads Per Kilobase of exon model per Million mapped reads. Defined as:<ref>Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL, Zhao
-Y, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA (2008). "Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells". ''Genome Res.'', '''18'''(4):610-21. PMID: 18285502. PMCID: PMC2279248.</ref>
+Y, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA (2008). "Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells". ''Genome Res.'', '''18'''(4):610-21. PMID 18285502. PMCID: PMC2279248.</ref>
 ::RPKM = totalExonReads / [ mappedReads(millions) * exonLengh(KB) ]
 :where,