Difference between revisions of "INF-BIOX121 H14 curriculum"
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FASTQ: Peter J. A. Cock et al<br/>Nucleic Acids Res. 2010 April; 38(6): 1767–1771<br/>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847217/ The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants] | FASTQ: Peter J. A. Cock et al<br/>Nucleic Acids Res. 2010 April; 38(6): 1767–1771<br/>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847217/ The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants] | ||
| − | <div>Noble WS (2009) [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000424 A Quick Guide to Organizing Computational Biology Projects]. PLoS Comput Biol 5(7): e1000424. doi:10.1371/journal.pcbi.1000424</div><div><br/></div><div><div>Wilson G, Aruliah DA, Brown CT, Chue Hong NP, Davis M, et al. (2014) [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001745 Best Practices for Scientific Computing]. PLoS Biol 12(1): e1001745. doi:10.1371/journal.pbio.1001745</div><div><br/></div><div><div>Sandve GK, Nekrutenko A, Taylor J, Hovig E (2013) [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003285 Ten Simple Rules for Reproducible Computational Research]. PLoS Comput Biol 9(10): e1003285. doi:10.1371/journal.pcbi.1003285 | + | <div><br/></div><div>Noble WS (2009) [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000424 A Quick Guide to Organizing Computational Biology Projects]. PLoS Comput Biol 5(7): e1000424. doi:10.1371/journal.pcbi.1000424</div><div><br/></div><div><div>Wilson G, Aruliah DA, Brown CT, Chue Hong NP, Davis M, et al. (2014) [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001745 Best Practices for Scientific Computing]. PLoS Biol 12(1): e1001745. doi:10.1371/journal.pbio.1001745</div><div><br/></div><div><div>Sandve GK, Nekrutenko A, Taylor J, Hovig E (2013) [http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003285 Ten Simple Rules for Reproducible Computational Research]. PLoS Comput Biol 9(10): e1003285. doi:10.1371/journal.pcbi.1003285</div></div></div> |
Latest revision as of 15:31, 14 October 2014
Required curriculum for credit students
The curriculum consists of these papers:
Sequencing technologies - the next generation
Metzker ML.
Nat Rev Genet. 2010 Jan;11(1):31-46
Tools for mapping high-throughput sequencing data
Fonseca NA, Rung J, Brazma A, Marioni JC.
Bioinformatics. 2012 Dec 15;28(24):3169-77.
A scaling normalization method for differential expression analysis of RNA-seq data.
Robinson MD, Oshlack A.
Genome Biol. 2010;11(3):R25.
Assembly algorithms for next-generation sequencing data
Miller JR, Koren S, Sutton G.
Genomics. 2010 Jun;95(6):315-27
ChIP-seq: advantages and challenges of a maturing technology
Park PJ.
Nat Rev Genet. 2009 Oct;10(10):669-80.
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
Goecks J, Nekrutenko A, Taylor J; Galaxy Team.
Genome Biol. 2010;11(8):R86.
The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment
De S, Pedersen BS, Kechris K.
Brief Bioinform. 2013 Aug 16.
RNA-Seq: a revolutionary tool for transcriptomics
Wang Z, Gerstein M, Snyder M.
Nat Rev Genet. 2009 Jan;10(1):57-63
Genotype and SNP calling from next-generation sequencing data
Nielsen R, Paul JS, Albrechtsen A, Song YS.
Nat Rev Genet. 2011 Jun;12(6):443-51.
Suggested reading
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
