sample names for each input SAM/BAM file. Use comma to separate multiple names, for example, sample_1, sample_2, sample_3. The number of sample names should be the same as the number of input SAM/BAM files.

Use this option to indicate how the input data has been sorted. The default is name.

Skip all reads with alignment quality lower than the given minimum value (default: 10)

Feature type (3rd column in GFF file) to be used, all features of other type are ignored (default, suitable for RNA-Seq analysis using an Ensembl GTF file: exon)

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. The default, suitable for RNA-Seq analysis using an Ensembl GTF file, is gene_id.

Mode to handle reads overlapping more than one feature. Possible values for are union, intersection-strict and intersection-nonempty (default: union)