Difference between revisions of "INF-BIOX121 H14 curriculum"
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− | + | == '''Required curriculum for credit students''' == | |
+ | <div> | ||
+ | The curriculum consists of these papers: | ||
+ | |||
+ | '''Sequencing technologies - the next generation. '''<br/>Metzker ML.<br/>Nat Rev Genet. 2010 Jan;11(1):31-46 | ||
+ | |||
+ | '''Tools for mapping high-throughput sequencing data. '''<br/>Fonseca NA, Rung J, Brazma A, Marioni JC.<br/>Bioinformatics. 2012 Dec 15;28(24):3169-77. | ||
+ | |||
+ | '''A scaling normalization method for differential expression analysis of RNA-seq data. '''<br/>Robinson MD, Oshlack A.<br/>Genome Biol. 2010;11(3):R25. | ||
+ | |||
+ | '''Assembly algorithms for next-generation sequencing data.'''<br/>Miller JR, Koren S, Sutton G.<br/>Genomics. 2010 Jun;95(6):315-27 | ||
+ | |||
+ | '''ChIP-seq: advantages and challenges of a maturing technology.'''<br/>Park PJ.<br/>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. '''<br/>Goecks J, Nekrutenko A, Taylor J; Galaxy Team.<br/>Genome Biol. 2010;11(8):R86. | ||
+ | |||
+ | '''The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment.'''<br/>De S, Pedersen BS, Kechris K.<br/>Brief Bioinform. 2013 Aug 16. | ||
+ | |||
+ | '''RNA-Seq: a revolutionary tool for transcriptomics. '''<br/>Wang Z, Gerstein M, Snyder M.<br/>Nat Rev Genet. 2009 Jan;10(1):57-63 | ||
+ | |||
+ | '''Genotype and SNP calling from next-generation sequencing data.'''<br/>Nielsen R, Paul JS, Albrechtsen A, Song YS.<br/>Nat Rev Genet. 2011 Jun;12(6):443-51. | ||
+ | |||
+ | |||
+ | <div>'''<span style="font-size: 12px;">Suggested reading</span>'''</div><div><br/></div><div><u>File formats</u></div> | ||
SAM (and BAM): [http://samtools.sourceforge.net/SAMv1.pdf "Sequence Alignment/Map Format Specification"] by "The SAM/BAM Format Specification Working Group" | SAM (and BAM): [http://samtools.sourceforge.net/SAMv1.pdf "Sequence Alignment/Map Format Specification"] by "The SAM/BAM Format Specification Working Group" | ||
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>More references will be added soon.</div> | + | <div>More references will be added soon.</div></div> |
Revision as of 22:57, 30 September 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.
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