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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]
* [[Protocols:GOstat_on_coexpression_cluster]]
* [Protocols:GOstat_on_MARA_motif_target]
* [[Protocols:GOstat_on_MARA_motif_target]]
* [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 16:50, 21 May 2012

Assay pipeline

Computational Pipeline

Computational analysis

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