SibeliaZ icon indicating copy to clipboard operation
SibeliaZ copied to clipboard
verified publisher icon medvedevgroup

sibeliaZ outputs

Open runxuan opened this issue 2 years ago • 8 comments

Hi,

on the Readme page, I have the impression that the output will contain two files, a GFF file "blocks_coords.gff" containing coordinates of the blocks, and file "alignment.maf" with the actual alignment.

However, i have run sibeliaz on my data twice and I only got "blocks_coords.gff" on both times with "alignment.maf" missing. There is no error message given. Have I done anything wrong here? any parameter needs to be turned on/off?

Also I want to generate a pan-genome graph in gfa format. I suppose this can be achieved through generating "alignment.maf"?

Thanks a lot!

Best regards,

Runxuan

runxuan avatar Apr 22 '23 07:04 runxuan

Hi,

This sounds like a bug. What is the dataset you are trying to align? Number of genomes, their size and type.

iminkin avatar Apr 27 '23 20:04 iminkin

Thanks a lot for your reply IIlia. I am aligning genomes from 20 different barley genotypes. Each barley genotype genome is around 5.1G bp in size. Barley is diploid with 7 chromosomes, but there are many unanchored fragments in addition in the fasta files.

Please let me know if you need further info.

Thanks

Runxuan

runxuan avatar May 04 '23 11:05 runxuan