...

HTSeq is set of tools for processing high-throughput sequencing data¹. In Partek Flow, we have implemented the htseq-count script from HTSeq for quantifying aligned reads to an annotation model. 

Invoking HTSeq

The input for HTSeq is an Aligned reads data node and a Gene/Feature annotation file.

To invoke run HTSeq,:

• Click an Aligned reads data node
• Click the Quantification section of the toolbox
• Click HTSeq

...

HTSeq outputs a Gene counts data node (Figure 2). 

References

1. Simon Anders, Paul Theodor Pyl, Wolfgang Huber. HTSeq — A Python framework to work with high-throughput sequencing data. Bioinformatics (2014), in print, online at doi:10.1093/bioinformatics/btu638

...