Protocols: Difference between revisions
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== Computational analysis == | == Computational analysis == | ||
* [[Protocols:CAGE_peak_calling]] | * [[Protocols:CAGE_peak_calling]] | ||
* | The Gene Ontology enrichment analysis for the following data sets | ||
* [[ | * Protocols:GOstat_on_coexpression_cluster | ||
* Protocols:GOstat_on_MARA_motif_target | |||
awas performed using GOstat ([[PMID:14962934]]) on gene lists with all known genes (human or mouse) as background. term significant at FDR 5% (Benjamin-Hochberg) were retained. | |||
* [[Protocols:Sample_enrichment_analysis_on_CAGE_peak_expression]] | * [[Protocols:Sample_enrichment_analysis_on_CAGE_peak_expression]] | ||
* [[Protocols:Sample_enrichment_analysis_on_coexpression_cluster]] | * [[Protocols:Sample_enrichment_analysis_on_coexpression_cluster]] | ||
* [[Protocols:Motif_Activity_Response_Analysis(MARA)]] | * [[Protocols:Motif_Activity_Response_Analysis(MARA)]] | ||
Revision as of 11:38, 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
- Protocols:GOstat_on_coexpression_cluster
- Protocols:GOstat_on_MARA_motif_target
awas performed using GOstat (PMID:14962934) on gene lists with all known genes (human or mouse) as background. term significant at FDR 5% (Benjamin-Hochberg) were retained.
