Chromosome tag

[ksc289]

Hi!!
I'm curated a genome with PretextView. I organized the map and tagged some unlocs with the M option and finally tagged the chromosomes with S mode. When I export the map to agp, a map.pretext.agp is generated, but in the first column only appears scaffolds, not chromosomes.
I don't know how can I obtain a .agp specifying which scaffolds form which chromosomes. Could you give me any idea?

Thank you very much,

Karen.

[additive3]

Hi @ksc289

Chromosome naming is done when the genome AGP is translated back to a FASTA file and is governed by what ever naming rules you use - size sorted or synteny for example.
You can set the AGP -> FASTA script to name these sequences as chr# or leave as scaffold_#
When submitting to INSDC through NCBI/ENA a chromosome designation list file is submitted along side you genome FASTA file.