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.

[debx4]

hello @ksc289 I would like to present ideas that are:
To generate a correct .agp file with chromosome information, make sure you properly tag scaffolds with the S mode in PretextView, assigning them to specific chromosomes. After organizing and tagging, export the map to an .agp file. If the exported .agp still only shows scaffolds in the first column, it means the chromosome-level tags were not saved correctly. You can either go back and re-tag the scaffolds or manually edit the .agp file to assign scaffolds to chromosomes following the AGP format. Ensure you use the latest version of PretextView to avoid potential issues.
I hope this will helpful. I would love for any further help , let me know .