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bioinfologics / satsuma2

FFT cross-correlation based synteny aligner, (re)designed to make full use of parallel computing
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Gene annotation after Chromosembler #28

Open lucasrocmoreira opened 4 years ago

lucasrocmoreira commented 4 years ago

Hi,

I am using Chromosembler to produce pseudochromosomes by mapping my scaffolds to the chromosome-level reference of a closely related species. An issue I'm facing is that after producing pseudochromosomes with Chromosembler I lose the gene annotation. I've tried to translate the coordinates from one reference to the other, but it does not seem to be very straightforward.

Do you have any suggestions/advice on how that can be done?

Thanks, Lucas

wuxingbo1986 commented 3 years ago

Hi Lucas,

I am doing something similar. Did you find a solution?

Thanks. Xingbo

lucasrocmoreira commented 3 years ago

Hi Xingbo,

I actually did. I found the easiest way to transfer the annotation is by using gmap (https://github.com/juliangehring/GMAP-GSNAP). gmap aligns back your protein sequences to the pseudochromosome reference generated by Chromosembler and outputs a new gff file.

I hope that helps.

Lucas

marchoeppner commented 1 year ago

Some of the developers (orig. Satsuma) have released a tool that basically uses Satsuma synteny chains to lift annotations between two assemblies (works also for distant relationships, btw). But obviously, this will not re-build your gene models to factor in any new information gained through the superscaffolding... so you might want to re-annotate anyway.

https://github.com/GrabherrGroup/kraken

Granted, the documentation is a bit sparse - so if you have any questions, let me know.

There is also a paper: https://pubmed.ncbi.nlm.nih.gov/24976580/