Partek Flow Documentation

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Numbered figure captions
SubtitleTextSpecify the .bedpe file for project projects started with counts matrix in Flow.
AnchorNamebedpe file

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A new datanode will be displayed as the task is finished. Double click on the output datanode, Flow will bring you to the IGV browser when where you could explore the “co-expressed”feature pairs (Figure 3).

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  • Sample name: name for each sample
  • Chromosome 1: the name of the chromosome on which the first end of the feature first feature exists.
  • Start 1: the zero-based starting position of the first end of the  feature on Chromosome 1that chromosome.
  • End 1: the zero-based ending position of the first end of the  feature on Chromosome 1that chromosome.
  • Chromosome 2: the name of the chromosome on which the second end of the  feature exists.
  • Start 2: the zero-based starting position of the second end of the  feature on Chromosome 2that chromosome.
  • End 2: the zero-based ending position of the second end of the  feature on Chromosome 2that chromosome.
  • Name: defines the name of the linkage features with the format of <name1><name2>, in which name1 and name2 are based on gene symbol or peak annotation. 
  • Score: linkage correlation, ranging from -1 to 1.
  • Strand 1:  all set to ".".
  • Strand 2:  all set to ".".
  • Significance: linkage significance: -log10 (p-value) after multiple testing correction (FDR, false discovery rate). Capped at 299.
  • Distance: distance in base pairs from feature 2 to feature 1.
  • Linkage type: can be "peak-peak", "gene-peak" or "peak-gene" depending on the type of gene or peak for feature 1 and feature 2.

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