Difference between revisions of "INF-BIOX121 H14 curriculum"

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<div>'''Required curriculum for credit students'''</div><div><br/></div><div>The curriculum will be added soon.</div><div><br/></div><div>'''<span style="font-size: 12px;">Suggested reading</span>'''</div><div><br/></div><div><u>File formats</u></div>
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== '''Required curriculum for credit students''' ==
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<div>
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The curriculum consists of these papers:
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'''Sequencing technologies - the next generation. '''<br/>Metzker ML.<br/>Nat Rev Genet. 2010 Jan;11(1):31-46
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'''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.
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'''A scaling normalization method for differential expression analysis of RNA-seq data. '''<br/>Robinson MD, Oshlack A.<br/>Genome Biol. 2010;11(3):R25.
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'''Assembly algorithms for next-generation sequencing data.'''<br/>Miller JR, Koren S, Sutton G.<br/>Genomics. 2010 Jun;95(6):315-27
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'''ChIP-seq: advantages and challenges of a maturing technology.'''<br/>Park PJ.<br/>Nat Rev Genet. 2009 Oct;10(10):669-80.
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'''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.
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'''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.
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'''RNA-Seq: a revolutionary tool for transcriptomics. '''<br/>Wang Z, Gerstein M, Snyder M.<br/>Nat Rev Genet. 2009 Jan;10(1):57-63
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'''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.
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<div>'''<span style="font-size: 12px;">Suggested reading</span>'''</div><div><br/></div><div><u>File formats</u></div>
 
SAM (and BAM):&nbsp;[http://samtools.sourceforge.net/SAMv1.pdf "Sequence Alignment/Map Format Specification"] by "The SAM/BAM Format Specification Working Group"
 
SAM (and BAM):&nbsp;[http://samtools.sourceforge.net/SAMv1.pdf "Sequence Alignment/Map Format Specification"] by "The SAM/BAM Format Specification Working Group"
  
 
FASTQ:&nbsp;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:&nbsp;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 21:57, 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.


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

More references will be added soon.