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Please note that HTSeq has not been optimized for performance and can take a very long time to run compared with Quantify to annotation model (Partek E/M) on the same data. 

Configurable options

The HTSeq includes basic configuration options for HTSeq include choosing the annotation file, the strand specificity, and whether to include all features from the annotation file on the main page and advanced options accessible by clicking Configure (Figure 1).

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