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:SmallRNAseq] | ||
* Protocols:RNAseq | * [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 | * [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 16:49, 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)]
