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The length of the bars labeled with blue and dark yellow in Fig 3 represents the quantitation of high-confidence mapped tags and all mapped tags, respectively.
2 3 The statistical results of the difference of methylation states in different genomic categories between two cell lines are presented, considering high confidence mapped tags and all mapped tags, respectively.
The depleted region could be ascribed to mapping ambiguities in these repeats which resulted in the removal of these multiply mapped tags, as typically only uniquely mapped tags are retained.
To apply this method for any ambiguous tag, the number of overlapping mapped tags at each of the possible ambiguous tag-mapped positions are counted and used to assign fractional weights to each possible position.
Only uniquely mapped tags were retained.
Only uniquely mapped tags were kept for downstream analyses.
Usually, researchers simply disregard ambiguous tags and only make use of uniquely mapped tags.
Total uniquely mapped tags were normalized to 10 million reads to generate tracks.
Datasets for different stages were normalized for the total number of uniquely mapped tags.
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Allowing for one mismatch in the P. enysii tags increased the percentage of mapped tags to 73 82% and the percentage of unambiguously mapping tags to 60 71%.
We therefore examined multi-mapped tags mapped to the duplicated promoter region.
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