mschatz
commented
2 years ago Hi Lara,
On Tue, May 10, 2022 at 3:31 PM Lara Pereira @.***> wrote:
Hello,
I ran Genomescope 2.0 on two HiFi datasets for two plant genomes. In both cases I get unexpected results and I am unsure of how to interpret them.
Genome 1:
http://genomescope.org/genomescope2.0/analysis.php?code=EUqq9F7CPpVQzDObKuPJ Genome size is about what I estimated by flow cytometry, but there is a tall error peak. The coverage is lower, though. Are these sequencing errors (shouldn't be that high in HiFi reads, I think)? Could it be due to sample contamination?
Yes, this looks weird to me. I would guess that first peak (around 10x coverage) is likely to be contamination of some kind. You could try assembling with hifiasm and then screening the contigs for those around this level. Then Id BLAST those contigs to see what they might be
Genome 2:
http://genomescope.org/genomescope2.0/analysis.php?code=1q4UixxtZ4acEF5YCQmQ Genome size is lower than what I estimated by flow cytometry. Also, there are only 20% unique seqs. Since I am not 100% sure of ploidy, I ran the model as if it was polyploid as well:
http://genomescope.org/genomescope2.0/analysis.php?code=MrIaUcE0wQuyNdqlEcGA Can we infer ploidy from this analysis? Do the four peaks suggest tetraploidy?
Yes, the 4 peaks strongly suggests tetraploid. The haplotypes are quite distinct so I would expect hifiasm to do a good job separating out the 4 haplotypes. Then I would try running BUSCO to look for core genes and expect most core genes will be in multiple copies (even though they are supposed to be just once).
Good luck!
Mike
Thank you for your help, Lara
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mrmrwinter
Hello,
I ran Genomescope 2.0 on two HiFi datasets for two plant genomes. In both cases I get unexpected results and I am unsure of how to interpret them.
Genome 1: http://genomescope.org/genomescope2.0/analysis.php?code=EUqq9F7CPpVQzDObKuPJ Genome size is about what I estimated by flow cytometry, but there is a tall error peak. The coverage is lower, though. Are these sequencing errors (shouldn't be that high in HiFi reads, I think)? Could it be due to sample contamination?
Genome 2: http://genomescope.org/genomescope2.0/analysis.php?code=1q4UixxtZ4acEF5YCQmQ Genome size is lower than what I estimated by flow cytometry. Also, there are only 20% unique seqs. Since I am not 100% sure of ploidy, I ran the model as if it was polyploid as well: http://genomescope.org/genomescope2.0/analysis.php?code=MrIaUcE0wQuyNdqlEcGA Can we infer ploidy from this analysis? Do the four peaks suggest tetraploidy?
Thank you for your help, Lara