Difference between revisions of "INF-BIOX120 H13 curriculum"

From projects/clsi
Jump to: navigation, search
(Added refs)
(Statistical genetics)
 
(6 intermediate revisions by 2 users not shown)
Line 20: Line 20:
  
 
== Suggested reading  ==
 
== Suggested reading  ==
 +
 +
=== File formats  ===
 +
 +
SAM (and BAM): [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]<br>
 +
 +
=== RNA-Seq  ===
 +
 +
Anders S et al.<br>Nat Protoc. 2013 Sep;8(9):1765-86<br>[http://www.ncbi.nlm.nih.gov/pubmed/23975260 Count-based differential expression analysis of RNA sequencing data using R and Bioconductor]<br>
 +
 +
<span style="line-height: 1.5em">Iyer MK &amp; Chinnaiyan AM.</span><br>Nat Biotechnol. 2011 Jul 11;29(7):599-600<br>[http://www.ncbi.nlm.nih.gov/pubmed/21747384 RNA-Seq unleashed]<br>
 +
 +
<span style="line-height: 1.5em">Trapnell C et al.</span><br>Nat Protoc. 2012 Mar 1;7(3):562-78<br>[http://www.ncbi.nlm.nih.gov/pubmed/22383036 Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks]<br>
  
 
=== Assembly  ===
 
=== Assembly  ===
  
Niranjan Nagarajan &amp; Mihai Pop<br>Nature Reviews Genetics 14, 157-167<br>[http://www.nature.com/nrg/journal/v14/n3/full/nrg3367.html Sequence assembly demystified]
+
Niranjan Nagarajan &amp; Mihai Pop<br>Nature Reviews Genetics 14, 157-167<br>[http://www.nature.com/nrg/journal/v14/n3/full/nrg3367.html Sequence assembly demystified]<br>
  
[http://www.nature.com/nrg/journal/v14/n3/full/nrg3367.html ]
+
Jason R. Miller, Sergey Koren and Granger Sutton<br>Genomics&nbsp;Volume 95, Issue 6, June 2010, Pages 315–327<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874646/ Assembly algorithms for next-generation sequencing data]<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 genomics ===
  
Jason R. Miller, Sergey Koren, Granger Sutton<br>Genomics&nbsp;Volume 95, Issue 6, June 2010, Pages 315–327<br>[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874646/ Assembly algorithms for next-generation sequencing data]<br>
+
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]  
  
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>
+
Sandve, Geir K., et al.&nbsp;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 09:47, 25 September 2013

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