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Protocols

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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)

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