what happens with htseq-count when several lines in a gff has the same ID?

Question

[caner]

Hi,

I have a custom gff file that uses same ID in the attributes field for some transcipts that can be expressed from several regions on the genome. I want the read counts of them to be combined. Is it how that work for htseq-count? Or does it report the counts for only one of those regions that share the same ID?

Thanks.

[mkulecka]

You can specify this with -i option. As htseq-count manual says it is "GFF attribute to be used as feature ID. Several GFF lines with the same feature ID will be considered as parts of the same feature. The feature ID is used to identity the counts in the output table."