Can I use one 2bit file with multiple query genomes?

[KabitaBaral1]

Hi, I am trying to run TOGA for Cactus 447 mammalian genomes. So far, I converted Cactus447.hal to fasta and then to 2bit. So, I have one 2bit for humans and one 2bit with all other 446 mammalian genomes. I do have separate chain files for each species. My question is: Do I need to generate individual 2bit files for each species, or can I use one 2bit file with all query species as my input?

Thank you

[MichaelHiller]

You don't need to extract 2bit files from the cactus Hal.
To generate a cactus alignment, you had all genomes either as fasta (then do faToTwoBit) or already as 2bit.

Important, one 2bit or fa file per genome.

[KabitaBaral1]

This helps a lot. Thank you, Michael. :)