Difference between revisions of "INF-BIOX120 H13 curriculum"
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Adam M Phillippy, Michael C Schatz and Mihai Pop<br>Genome Biology 2008, 9:R55<br>[http://genomebiology.com/content/9/3/R55 Genome assembly forensics: finding the elusive mis-assembly]<br> | Adam M Phillippy, Michael C Schatz and Mihai Pop<br>Genome Biology 2008, 9:R55<br>[http://genomebiology.com/content/9/3/R55 Genome assembly forensics: finding the elusive mis-assembly]<br> | ||
− | === Statistical | + | === Statistical genomics === |
− | Goecks, Jeremy, et al. Genome Biol 11.8 (2010): R86 [http://www.biomedcentral.com/content/pdf/gb-2010-11-8-r86.pdf Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences] | + | Goecks, Jeremy, et al. Genome Biol 11.8 (2010): R86 [http://www.biomedcentral.com/content/pdf/gb-2010-11-8-r86.pdf Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences] |
− | Sandve, Geir K., et al. Nucleic acids res. (2013) | + | Sandve, Geir K., et al. Nucleic acids res. (2013) [http://nar.oxfordjournals.org/content/41/W1/W133 The Genomic HyperBrowser: an analysis web server for genome-scale data] |
Latest revision as of 10:47, 25 September 2013
Contents
Required curriculum for credit students
The curriculum consists of these four papers:
Metzker, ML
Nat Rev Genet. 2010 Jan;11(1):31-46
Sequencing technologies - the next generation.
Nielsen R, Paul JS, Albrechtsen A, Song YS.
Nat Rev Genet. 2011 Jun;12(6):443-51
Genotype and SNP calling from next-generation sequencing data.
Oshlack A, Robinson MD, Young MD.
Genome Biol. 2010;11(12):220
From RNA-seq reads to differential expression results.
Flicek P, Birney E.
Nat Methods. 2009 Nov;6
Sense from sequence reads : methods for alignment and assembly
Suggested reading
File formats
SAM (and BAM): "Sequence Alignment/Map Format Specification" by "The SAM/BAM Format Specification Working Group"
FASTQ: Peter J. A. Cock et al
Nucleic Acids Res. 2010 April; 38(6): 1767–1771
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
RNA-Seq
Anders S et al.
Nat Protoc. 2013 Sep;8(9):1765-86
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
Iyer MK & Chinnaiyan AM.
Nat Biotechnol. 2011 Jul 11;29(7):599-600
RNA-Seq unleashed
Trapnell C et al.
Nat Protoc. 2012 Mar 1;7(3):562-78
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Assembly
Niranjan Nagarajan & Mihai Pop
Nature Reviews Genetics 14, 157-167
Sequence assembly demystified
Jason R. Miller, Sergey Koren and Granger Sutton
Genomics Volume 95, Issue 6, June 2010, Pages 315–327
Assembly algorithms for next-generation sequencing data
Adam M Phillippy, Michael C Schatz and Mihai Pop
Genome Biology 2008, 9:R55
Genome assembly forensics: finding the elusive mis-assembly
Statistical genomics
Goecks, Jeremy, et al. Genome Biol 11.8 (2010): R86 Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
Sandve, Geir K., et al. Nucleic acids res. (2013) The Genomic HyperBrowser: an analysis web server for genome-scale data