NAME¶

flattenGTF - Flatten features included in a GTF annotation and save the modified annotation to a SAF format file.

USAGE¶

flattenGTF [options] -a <input_file> -o <output_file>

## Mandatory arguments:

-a <file>

Name of an annotation file in GTF/GFF format.

-o <file>

Name of output file.

## Optional arguments:

-t <string>

Specify feature type in a GTF annotation. 'exon' by default. Features with the specified feature type are extracted from the annotation for processing.

-g <string>

Specify attribute type in GTF annotation. 'gene_id' by default. This attribute type is used to group features into metafeatures.

-C

Merging overlapping exons into multiple non-overlapping exons but all the edges are kept.