Convert coordinates from one cotton genome to another

Question

[kspata]

Greetings,

I have a small multifasta file (target) belonging to a cotton genome. I need to lift over the positions from one cotton genome (target) to another (Reference). The headers of the target fasta file are different than the reference file.

Is there any way I can achieve this using the target and reference fasta files only?

I looked at UCSC liftover and NCBI Remap, but both support only specific references and cotton is not one of them.

Would appreciate the help.

Thanks in advance !!

[lieven.sterck]

perhaps liftoff from the salzberg group could prove useful? alternatives are RATT (mainly bacterial) , lift-over from the ALLMAPS package