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

To run HTSeq:

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

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Depending on the library preparation method, information about the strand of the original transcript may be faithfully preserved or lost. This setting controls whether HTSeq considers strand during quantification. Consult your library preparation method user manual if you are unsure about if and how the method preserved strand information. 

If set to noto no, a read is considered to be overlapping a feature regardless of whether it maps to the same or opposite strand as the feature.

If set to yes, the read has to be matched to the same strand as the feature if single-end reads and matched to the same strand for the first read and the opposite strand for the second read if paired-end reads. 

If set to reverse, the read has to be matched to the opposite strand as the feature if single-end reads and matched to the opposite strand for the first read and the same strand for the second read if paired-end reads.

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This option determines how HTSeq handles reads that partially overlap features. The default is union. 

If set to union, any read that is partially overlapped by a feature will be assigned to that feature. Assignment is non-exclusive if multiple feature overlap. 

If set to intersection-strict, only reads that are fully overlapped by a feature will be assigned to that feature. Assignment is non-exclusive if multiple feature fully overlap. 

If set to intersection-nonempty, reads are assigned to the feature that has the greatest overlap. Assignment is non-exclusive if multiple feature overlap the same amount. 

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This option determines how HTSeq counts reads that are assigned to more than one feature. The default is none.

If set to none, reads that are assigned to more than one feature are not counted for any feature.

If set to all, reads are counted for all features they are assigned to. 

Output

HTSeq outputs a Gene counts data node (Figure 3). There is no task report. 

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