Protocols: Difference between revisions
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== Assay pipeline == | == Assay pipeline == | ||
* [Protocols:RNA_extraction] | * [[Protocols:RNA_extraction]] | ||
* [Protocols:HeliScopeCAGE] | * [[Protocols:HeliScopeCAGE]] | ||
* [Protocols:Low_quantity_HeliScopeCAGE] | * [[Protocols:Low_quantity_HeliScopeCAGE]] | ||
* [Protocols:SmallRNAseq] | * [[Protocols:nanoCAGEscan]] | ||
* [Protocols:RNAseq] | * [[Protocols:SmallRNAseq]] | ||
* [[Protocols:RNAseq]] | |||
== Computational Pipeline == | == Computational Pipeline == | ||
* [Protocols:rRNAdust] | * [[Protocols:rRNAdust]] | ||
* [Protocols:HeliScopeCAGE_read_alignment] - delve, filtering (Q20 + percent identity), CTSS | * [[Protocols:HeliScopeCAGE_read_alignment]] - delve, filtering (Q20 + percent identity), CTSS | ||
* [Protocols:RNAseq_read_alignment] - TopHat, Cufflinks, (Trinity), Cuffmerge | * [[Protocols:RNAseq_read_alignment]] - TopHat, Cufflinks, (Trinity), Cuffmerge | ||
* [Protocols:SmallRNAseq_read_alignment] - BWA | * [[Protocols:SmallRNAseq_read_alignment]] - BWA | ||
== Computational analysis == | == Computational analysis == | ||
* [Protocols:CAGE_peak_calling] | * [[Protocols:CAGE_peak_calling]] | ||
* | The Gene Ontology enrichment analysis for the following data sets | ||
* | * GOstat_on_coexpression_cluster | ||
* [Protocols:Sample_enrichment_analysis_on_CAGE_peak_expression] | * GOstat_on_MARA_motif_target | ||
* [Protocols:Sample_enrichment_analysis_on_coexpression_cluster] | was performed using GOstat (PMID:14962934) on gene lists with all known genes (human or mouse) as background. Terms significant at FDR 5% (Benjamin-Hochberg) were retained. | ||
* [Protocols:Motif_Activity_Response_Analysis(MARA)] | * [[Protocols:Sample_enrichment_analysis_on_CAGE_peak_expression]] | ||
* [[Protocols:Sample_enrichment_analysis_on_coexpression_cluster]] | |||
* [[Protocols:Motif_Activity_Response_Analysis(MARA)]] | |||
Latest revision as of 13:55, 3 September 2012
Assay pipeline
- Protocols:RNA_extraction
- Protocols:HeliScopeCAGE
- Protocols:Low_quantity_HeliScopeCAGE
- Protocols:nanoCAGEscan
- Protocols:SmallRNAseq
- Protocols:RNAseq
Computational Pipeline
- Protocols:rRNAdust
- Protocols:HeliScopeCAGE_read_alignment - delve, filtering (Q20 + percent identity), CTSS
- Protocols:RNAseq_read_alignment - TopHat, Cufflinks, (Trinity), Cuffmerge
- Protocols:SmallRNAseq_read_alignment - BWA
Computational analysis
The Gene Ontology enrichment analysis for the following data sets
- GOstat_on_coexpression_cluster
- GOstat_on_MARA_motif_target
was performed using GOstat (PMID:14962934) on gene lists with all known genes (human or mouse) as background. Terms significant at FDR 5% (Benjamin-Hochberg) were retained.
