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] | ||
Revision as of 16:49, 21 May 2012
Assay pipeline
- Protocols:RNA_extraction
- [Protocols:HeliScopeCAGE]
- [Protocols:Low_quantity_HeliScopeCAGE]
- [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
- [Protocols:CAGE_peak_calling]
- [Protocols:GOstat_on_coexpression_cluster]
- [Protocols:GOstat_on_MARA_motif_target]
- [Protocols:Sample_enrichment_analysis_on_CAGE_peak_expression]
- [Protocols:Sample_enrichment_analysis_on_coexpression_cluster]
- [Protocols:Motif_Activity_Response_Analysis(MARA)]
