Galaxy DNA-Seq Tutorial - Revision history

Ozborn@uab.edu: /* Comparative Genomics */

2011-09-16T14:19:18Z

Comparative Genomics

← Older revision		Revision as of 14:19, 16 September 2011
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	The left portion of the results file is shown below.		The left portion of the results file is shown below.
	[[File:SNPEffResultTabular.jpg]]		[[File:SNPEffResultTabular.jpg]]

			=== SNP Effect Again (optional ===
			Return SNPEff on the smaller dataset

	== Viewing results in IGV ==		== Viewing results in IGV ==

2011-09-16T14:17:50Z

Difference from consensus

← Older revision		Revision as of 14:17, 16 September 2011
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	== Difference from consensus ==		== Difference from consensus ==
	Now take only changes which result in a change from the consensus.		Now take only changes which result in a change from the consensus.

			* Select Filter and Sort -> Filter

	[[File:FilterRunVacWR.jpg]]		[[File:FilterRunVacWR.jpg]]

2011-09-16T14:16:04Z

SNPEff - Variation Summation (optional)

← Older revision		Revision as of 14:16, 16 September 2011
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	[[File:GalaxyTutorialSharedLibrary.jpg]]		[[File:GalaxyTutorialSharedLibrary.jpg]]

	== SNPEff - Variation Summation (optional) ==		== SNP Effect (SNPEff) - Variation Summation (optional) ==
	Summarizing variants and effects of SNPs.		Summarizing variants and effects of SNPs.
	* Reference genome must be in SNPEff, need GFF3 file of your genome annotation		* Reference genome must be in SNPEff, need GFF3 file of your genome annotation

2011-09-16T14:15:20Z

Comparative Genomics

← Older revision		Revision as of 14:15, 16 September 2011
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	[[File:FilterRunVacWR.jpg]]		[[File:FilterRunVacWR.jpg]]

	=== Comparative Genomics ===		== Comparative Genomics ==
	To review, the VAC-WR strain is the progenitor (parent) of the other two strains. It does not have a phenotype of interest. Thus we are only interested in genomic differences between our two mutants strains and the parent strain. Differences between the reference NCBI strain are not of interest if they also appear in the parent strain.		To review, the VAC-WR strain is the progenitor (parent) of the other two strains. It does not have a phenotype of interest. Thus we are only interested in genomic differences between our two mutants strains and the parent strain. Differences between the reference NCBI strain are not of interest if they also appear in the parent strain.

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	[[File:CMV21950RvsVACWR CompareData.jpg]]		[[File:CMV21950RvsVACWR CompareData.jpg]]


	=== Result File ===		=== Result File ===

2011-09-16T14:14:54Z

Difference from consensus

← Older revision		Revision as of 14:14, 16 September 2011
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	If this runs but gives an empty result, it may be because Galaxy believes the pileup files are in tabular format. Fix this.		If this runs but gives an empty result, it may be because Galaxy believes the pileup files are in tabular format. Fix this.

	=== Difference from consensus ===		== Difference from consensus ==
	Now take only changes which result in a change from the consensus.		Now take only changes which result in a change from the consensus.

	[[File:FilterRunVacWR.jpg]]		[[File:FilterRunVacWR.jpg]]


	=== Comparative Genomics ===		=== Comparative Genomics ===

2011-09-16T14:14:41Z

Pileup Filter

← Older revision		Revision as of 14:14, 16 September 2011
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	* Previous knowledge		* Previous knowledge

	=== Pileup Filter ===		== Pileup Filter ==
	For the tutorial here, I selected a quality cutoff of 20 and a minimum coverage of 100 reads.		For the tutorial here, I selected a quality cutoff of 20 and a minimum coverage of 100 reads.
	* Filter all 3 pileups		* Filter all 3 pileups

2011-09-16T14:14:01Z

Finding the Relevant SNPs versus Control

← Older revision		Revision as of 14:14, 16 September 2011
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	[[File:SNPEffResults.jpg]]		[[File:SNPEffResults.jpg]]

	=== Finding the Relevant SNPs versus Control ===		== Finding the Relevant SNPs versus Control ==
	Too many SNPs! We need to make some decisions as to what to include and exclude. This is an active area of research, answer depends on:		Too many SNPs! We need to make some decisions as to what to include and exclude. This is an active area of research, answer depends on:
	* Overall coverage		* Overall coverage

2011-09-16T08:18:23Z

Galaxy DNA-Seq Tutorial

← Older revision		Revision as of 08:18, 16 September 2011
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	= Galaxy DNA-Seq Tutorial =		= Galaxy DNA-Seq Tutorial =

			Presentation [[media:RCD2011_DNA-Seq_Workshop_Talk.pdf‎\|PDF]] or original [ftp://ftp.genome.uab.edu/ICS/Galaxy_RNAseq_tutorial/RCD2011%20DNA-Seq%20Workshop%20Talk.pptx PPTX] from HPC Boot Camp 2011.


	== Linking to data ==		== Linking to data ==

2011-09-16T06:46:55Z

Pileup Filter

← Older revision		Revision as of 06:46, 16 September 2011
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	[[File:PileupFiltering100Reads.jpg]]		[[File:PileupFiltering100Reads.jpg]]

			If this runs but gives an empty result, it may be because Galaxy believes the pileup files are in tabular format. Fix this.

	=== Difference from consensus ===		=== Difference from consensus ===

2011-09-16T06:45:31Z

SNPEff - Variation Summation

← Older revision		Revision as of 06:45, 16 September 2011
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	[[File:GalaxyTutorialSharedLibrary.jpg]]		[[File:GalaxyTutorialSharedLibrary.jpg]]

	== SNPEff - Variation Summation ==		== SNPEff - Variation Summation (optional) ==
	Summarizing variants and effects of SNPs.		Summarizing variants and effects of SNPs.
	* Reference genome must be in SNPEff, need GFF3 file of your genome annotation		* Reference genome must be in SNPEff, need GFF3 file of your genome annotation
Line 234:		Line 234:
	The left portion of the results file is shown below.		The left portion of the results file is shown below.
	[[File:SNPEffResultTabular.jpg]]		[[File:SNPEffResultTabular.jpg]]


	== Viewing results in IGV ==		== Viewing results in IGV ==