Table 1:
Options for GAG
| Option | Type of function | Description |
|---|---|---|
| -a <annotation file> | Annotate | Adds functional annotations present in annotation file to .gff and .tbl |
| -t <.bed file> | Trim | Removes regions of genome indicated in .bed file from .fasta and .gff3 |
| -fix_start_stop <no value> | Fix | Adds or corrects start and stop codon features to .gff3 |
| -fix_terminal_ns <no value> | Fix | Removes any trailing ends from contig ends in assembly, updates .gff3 coordinates |
| -rcs <integer> | Remove | Remove CDS shorter than <integer> |
| -rcl <integer> | Remove | Remove CDS longer than <integer> |
| -res <integer> | Remove | Remove exons shorter than <integer> |
| -rel <integer> | Remove | Remove exons longer than <integer> |
| -ris <integer> | Remove | Remove introns shorter than <integer> |
| -ril <integer> | Remove | Remove introns longer than <integer> |
| -rgs <integer> | Remove | Remove genes shorter than <integer> |
| -rgl <integer> | Remove | Remove genes longer than <integer> |
| -fcs <integer> | Flag | Flag CDS shorter than <integer> |
| -fcl <integer> | Flag | Flag CDS longer than <integer> |
| -fes <integer> | Flag | Flag exons shorter than <integer> |
| -fel <integer> | Flag | Flag exons longer than <integer> |
| -fis <integer> | Flag | Flag introns shorter than <integer> |
| -fil <integer> | Flag | Flag introns longer than <integer> |
| -fgs <integer> | Flag | Flag genes shorter than <integer> |
| -fgl <integer> | Flag | Flag genes longer than <integer> |