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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]]
* [Protocols:GOstat_on_coexpression_cluster]
The Gene Ontology enrichment analysis for the following data sets
* [Protocols:GOstat_on_MARA_motif_target]
* 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

Computational Pipeline

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.