16 gene annotation

-a Name of an annotation file (gzipped file is accepted). GTF/GFF format by default. See -F option for more format information.

-F Specify format of the provided annotation file. Acceptable formats include ‘GTF’ (or compatible GFF format) and ‘SAF’. ‘GTF’ by default. For SAF format, please refer to Users Guide.

-A Provide a chromosome name alias file to match chr names in annotation with those in the reads. This should be a two- column comma-delimited text file. Its first column should include chr names in the annotation and its second column should include chr names in the index. Chr names are case sensitive. No column header should be included in the file.

–gtfFeature Specify feature type in GTF annotation. ‘exon’ by default. Features used for read counting will be extracted from annotation using the provided value.

–gtfAttr Specify attribute type in GTF annotation. ‘gene_id’ by default. Meta-features used for read counting will be extracted from annotation using the provided value.