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11) The PCR based amplification process for mRNA library synthesis may generate ‘duplicate reads’, which can potentially lead to artefacts. The application of this algorithm allows the removal of duplicate reads in real time. It is not a real filter sensu stricto. Its application removes the duplicate reads and thus decreases the coverage and score variables (possibly modifying also annotations such as the Junction evidence) for all the candidate fusions positive for the presence of duplicate reads. If used in combination with filtering algorithms, such as the threshold filter, it can be very potent in order to detect and eliminate artefacts.
12) Not a filter: it regulates the minimum alpha channel transparency of each fusion in the Visualization Module. By default, it is proportional to the overall score of each fusion. It is often useful to increase (or decrease) the sharpness of low scoring fusions.
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