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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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